Starting phenix.real_space_refine
on Thu Mar  5 04:32:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6u9f_20696/03_2026/6u9f_20696.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6u9f_20696/03_2026/6u9f_20696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6u9f_20696/03_2026/6u9f_20696.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6u9f_20696/03_2026/6u9f_20696.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6u9f_20696/03_2026/6u9f_20696.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6u9f_20696/03_2026/6u9f_20696.cif"
  }
  resolution = 4.35
  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=   0.004
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      36      5.16       5
     C   12081      2.51       5
     N    3273      2.21       5
     O    3789      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 19179
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 717, 5399
          Classifications: {'peptide': 717}
          Incomplete info: {'truncation_to_alanine': 139}
          Link IDs: {'CIS': 6, 'PTRANS': 19, 'TRANS': 691}
          Chain breaks: 11
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 491
          Unresolved non-hydrogen angles: 625
          Unresolved non-hydrogen dihedrals: 404
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'ASP:plan': 11, 'ASN:plan1': 14, 'GLN:plan1': 3, 'GLU:plan': 3, 'PHE:plan': 3, 'TYR:plan': 11, 'ARG:plan': 6, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 239
    Chain: "B"
      Number of atoms: 994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 994
          Classifications: {'peptide': 133}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'CIS': 1, 'TRANS': 131}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
  Restraints were copied for chains:
    C, E, D, F
  Time building chain proxies: 4.35, per 1000 atoms: 0.23
  Number of scatterers: 19179
  At special positions: 0
  Unit cell: (103.79, 103.79, 243.96, 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      36     16.00
     O    3789      8.00
     N    3273      7.00
     C   12081      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 713.7 milliseconds
  

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4974

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 36 sheets defined
      18.1% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
      removed outlier: 3.608A  pdb=" N   THR A   8 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP A   9 " --> pdb=" O   LYS A   5 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 4 through 9'
    Processing helix  chain 'A' and resid 28 through 36
      removed outlier: 3.999A  pdb=" N   ALA A  33 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LYS A  34 " --> pdb=" O   PRO A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 52
      removed outlier: 4.201A  pdb=" N   SER A  49 " --> pdb=" O   ASN A  45 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN A  50 " --> pdb=" O   TYR A  46 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 86
      removed outlier: 3.601A  pdb=" N   LEU A  69 " --> pdb=" O   TYR A  65 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   SER A  71 " --> pdb=" O   LYS A  67 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TYR A  75 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A  78 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 107
    Processing helix  chain 'A' and resid 125 through 146
      removed outlier: 3.679A  pdb=" N   ILE A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG A 133 " --> pdb=" O   HIS A 129 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 158
    Processing helix  chain 'A' and resid 158 through 166
    Processing helix  chain 'A' and resid 246 through 254
      removed outlier: 4.007A  pdb=" N   ASN A 251 " --> pdb=" O   HIS A 247 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   PHE A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 336
      removed outlier: 4.108A  pdb=" N   LYS A 336 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 354
    Processing helix  chain 'A' and resid 387 through 399
      removed outlier: 3.642A  pdb=" N   LEU A 396 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASN A 399 " --> pdb=" O   GLN A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 428
      removed outlier: 3.571A  pdb=" N   GLN A 427 " --> pdb=" O   ASP A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 581
      removed outlier: 3.810A  pdb=" N   GLN A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 578 " --> pdb=" O   CYS A 574 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   TYR A 579 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 776
      removed outlier: 3.771A  pdb=" N   GLU A 775 " --> pdb=" O   GLY A 772 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ASN A 776 " --> pdb=" O   SER A 773 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 772 through 776'
    Processing helix  chain 'C' and resid 4 through 9
      removed outlier: 3.608A  pdb=" N   THR C   8 " --> pdb=" O   VAL C   4 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP C   9 " --> pdb=" O   LYS C   5 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 4 through 9'
    Processing helix  chain 'C' and resid 28 through 36
      removed outlier: 3.999A  pdb=" N   ALA C  33 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LYS C  34 " --> pdb=" O   PRO C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 52
      removed outlier: 4.200A  pdb=" N   SER C  49 " --> pdb=" O   ASN C  45 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ASN C  50 " --> pdb=" O   TYR C  46 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN C  52 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 86
      removed outlier: 3.601A  pdb=" N   LEU C  69 " --> pdb=" O   TYR C  65 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   SER C  71 " --> pdb=" O   LYS C  67 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR C  75 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR C  78 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 107
    Processing helix  chain 'C' and resid 125 through 146
      removed outlier: 3.679A  pdb=" N   ILE C 132 " --> pdb=" O   PRO C 128 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG C 133 " --> pdb=" O   HIS C 129 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS C 134 " --> pdb=" O   ASP C 130 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU C 139 " --> pdb=" O   ILE C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 158
    Processing helix  chain 'C' and resid 158 through 166
    Processing helix  chain 'C' and resid 246 through 254
      removed outlier: 4.006A  pdb=" N   ASN C 251 " --> pdb=" O   HIS C 247 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   PHE C 252 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU C 253 " --> pdb=" O   ASP C 249 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU C 254 " --> pdb=" O   PHE C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 328 through 336
      removed outlier: 4.107A  pdb=" N   LYS C 336 " --> pdb=" O   ALA C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 354
    Processing helix  chain 'C' and resid 387 through 399
      removed outlier: 3.642A  pdb=" N   LEU C 396 " --> pdb=" O   PHE C 392 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN C 399 " --> pdb=" O   GLN C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 428
      removed outlier: 3.570A  pdb=" N   GLN C 427 " --> pdb=" O   ASP C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 573 through 581
      removed outlier: 3.809A  pdb=" N   GLN C 577 " --> pdb=" O   TYR C 573 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU C 578 " --> pdb=" O   CYS C 574 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   TYR C 579 " --> pdb=" O   SER C 575 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 772 through 776
      removed outlier: 3.771A  pdb=" N   GLU C 775 " --> pdb=" O   GLY C 772 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ASN C 776 " --> pdb=" O   SER C 773 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 772 through 776'
    Processing helix  chain 'E' and resid 4 through 9
      removed outlier: 3.609A  pdb=" N   THR E   8 " --> pdb=" O   VAL E   4 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP E   9 " --> pdb=" O   LYS E   5 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 4 through 9'
    Processing helix  chain 'E' and resid 28 through 36
      removed outlier: 3.999A  pdb=" N   ALA E  33 " --> pdb=" O   THR E  29 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LYS E  34 " --> pdb=" O   PRO E  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 52
      removed outlier: 4.201A  pdb=" N   SER E  49 " --> pdb=" O   ASN E  45 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ASN E  50 " --> pdb=" O   TYR E  46 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 86
      removed outlier: 3.601A  pdb=" N   LEU E  69 " --> pdb=" O   TYR E  65 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   SER E  71 " --> pdb=" O   LYS E  67 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR E  75 " --> pdb=" O   SER E  71 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS E  77 " --> pdb=" O   LEU E  73 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR E  78 " --> pdb=" O   ASP E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 107
    Processing helix  chain 'E' and resid 125 through 146
      removed outlier: 3.679A  pdb=" N   ILE E 132 " --> pdb=" O   PRO E 128 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG E 133 " --> pdb=" O   HIS E 129 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS E 134 " --> pdb=" O   ASP E 130 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU E 139 " --> pdb=" O   ILE E 135 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 158
    Processing helix  chain 'E' and resid 158 through 166
    Processing helix  chain 'E' and resid 246 through 254
      removed outlier: 4.006A  pdb=" N   ASN E 251 " --> pdb=" O   HIS E 247 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   PHE E 252 " --> pdb=" O   LYS E 248 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU E 253 " --> pdb=" O   ASP E 249 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU E 254 " --> pdb=" O   PHE E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 328 through 336
      removed outlier: 4.107A  pdb=" N   LYS E 336 " --> pdb=" O   ALA E 332 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 347 through 354
    Processing helix  chain 'E' and resid 387 through 399
      removed outlier: 3.642A  pdb=" N   LEU E 396 " --> pdb=" O   PHE E 392 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN E 399 " --> pdb=" O   GLN E 395 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 423 through 428
      removed outlier: 3.572A  pdb=" N   GLN E 427 " --> pdb=" O   ASP E 423 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 573 through 581
      removed outlier: 3.809A  pdb=" N   GLN E 577 " --> pdb=" O   TYR E 573 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU E 578 " --> pdb=" O   CYS E 574 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   TYR E 579 " --> pdb=" O   SER E 575 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 772 through 776
      removed outlier: 3.771A  pdb=" N   GLU E 775 " --> pdb=" O   GLY E 772 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ASN E 776 " --> pdb=" O   SER E 773 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 772 through 776'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215
      removed outlier: 3.852A  pdb=" N   GLU A 181 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASN A 267 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 327
      removed outlier: 3.876A  pdb=" N   GLY A 235 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASN A 234 " --> pdb=" O   CYS A 227 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 224 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG A 564 " --> pdb=" O   GLU A 228 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ILE A 561 " --> pdb=" O   LYS A 618 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LYS A 618 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLN A 563 " --> pdb=" O   LYS A 616 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS A 616 " --> pdb=" O   GLN A 563 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS A 565 " --> pdb=" O   THR A 614 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 614 " --> pdb=" O   LYS A 565 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS A 569 " --> pdb=" O   ASP A 610 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR A 615 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A 525 " --> pdb=" O   TYR A 615 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLU A 522 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241
    Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 346
      removed outlier: 3.534A  pdb=" N   ASN A 345 " --> pdb=" O   PRO A 377 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 363 through 365
      removed outlier: 7.480A  pdb=" N   SER A 363 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 9.081A  pdb=" N   VAL A 418 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   ASP A 365 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   HIS A 417 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL A 419 " --> pdb=" O   TYR A 402 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 464
      removed outlier: 6.239A  pdb=" N   LYS A 464 " --> pdb=" O   PHE A 492 " (cutoff:3.500A)
      removed outlier: 8.902A  pdb=" N   SER A 494 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 466 through 467
      removed outlier: 3.501A  pdb=" N   GLU A 480 " --> pdb=" O   ASN A 467 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 637 through 640
      removed outlier: 6.725A  pdb=" N   LEU A 736 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LYS A 744 " --> pdb=" O   GLN A 740 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 692 through 695
      removed outlier: 3.570A  pdb=" N   LEU A 713 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 779 through 781
      removed outlier: 3.601A  pdb=" N   SER A 802 " --> pdb=" O   ARG A 814 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ARG A 814 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 804 " --> pdb=" O   PHE A 812 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP B  18 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU B  15 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   THR B  37 " --> pdb=" O   LYS B  29 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LYS B  35 " --> pdb=" O   GLU B  31 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ILE B  36 " --> pdb=" O   GLU F  45 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   SER F  47 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   HIS B  38 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASN D  55 " --> pdb=" O   SER F  46 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER D  75 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER D  76 " --> pdb=" O   LYS D  87 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE D  86 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE D  88 " --> pdb=" O   SER D  91 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 214 through 215
      removed outlier: 3.852A  pdb=" N   GLU C 181 " --> pdb=" O   ASN C 267 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASN C 267 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 327
      removed outlier: 3.876A  pdb=" N   GLY C 235 " --> pdb=" O   PHE C 326 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASN C 234 " --> pdb=" O   CYS C 227 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU C 224 " --> pdb=" O   PHE C 568 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG C 564 " --> pdb=" O   GLU C 228 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   ILE C 561 " --> pdb=" O   LYS C 618 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LYS C 618 " --> pdb=" O   ILE C 561 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLN C 563 " --> pdb=" O   LYS C 616 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LYS C 616 " --> pdb=" O   GLN C 563 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS C 565 " --> pdb=" O   THR C 614 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR C 614 " --> pdb=" O   LYS C 565 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS C 569 " --> pdb=" O   ASP C 610 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR C 615 " --> pdb=" O   LEU C 525 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU C 525 " --> pdb=" O   TYR C 615 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLU C 522 " --> pdb=" O   ILE C 455 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 240 through 241
    Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 346
      removed outlier: 3.534A  pdb=" N   ASN C 345 " --> pdb=" O   PRO C 377 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 363 through 365
      removed outlier: 7.480A  pdb=" N   SER C 363 " --> pdb=" O   TYR C 416 " (cutoff:3.500A)
      removed outlier: 9.080A  pdb=" N   VAL C 418 " --> pdb=" O   SER C 363 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   ASP C 365 " --> pdb=" O   VAL C 418 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS C 417 " --> pdb=" O   LYS C 404 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL C 419 " --> pdb=" O   TYR C 402 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 461 through 464
      removed outlier: 6.239A  pdb=" N   LYS C 464 " --> pdb=" O   PHE C 492 " (cutoff:3.500A)
      removed outlier: 8.901A  pdb=" N   SER C 494 " --> pdb=" O   LYS C 464 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 466 through 467
      removed outlier: 3.502A  pdb=" N   GLU C 480 " --> pdb=" O   ASN C 467 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 637 through 640
      removed outlier: 6.724A  pdb=" N   LEU C 736 " --> pdb=" O   ILE C 748 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LYS C 744 " --> pdb=" O   GLN C 740 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 692 through 695
      removed outlier: 3.570A  pdb=" N   LEU C 713 " --> pdb=" O   TYR C 692 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 779 through 781
      removed outlier: 3.601A  pdb=" N   SER C 802 " --> pdb=" O   ARG C 814 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ARG C 814 " --> pdb=" O   SER C 802 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU C 804 " --> pdb=" O   PHE C 812 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 214 through 215
      removed outlier: 3.852A  pdb=" N   GLU E 181 " --> pdb=" O   ASN E 267 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASN E 267 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 324 through 327
      removed outlier: 3.876A  pdb=" N   GLY E 235 " --> pdb=" O   PHE E 326 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASN E 234 " --> pdb=" O   CYS E 227 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU E 224 " --> pdb=" O   PHE E 568 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG E 564 " --> pdb=" O   GLU E 228 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   ILE E 561 " --> pdb=" O   LYS E 618 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LYS E 618 " --> pdb=" O   ILE E 561 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLN E 563 " --> pdb=" O   LYS E 616 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LYS E 616 " --> pdb=" O   GLN E 563 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS E 565 " --> pdb=" O   THR E 614 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR E 614 " --> pdb=" O   LYS E 565 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS E 569 " --> pdb=" O   ASP E 610 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR E 615 " --> pdb=" O   LEU E 525 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU E 525 " --> pdb=" O   TYR E 615 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLU E 522 " --> pdb=" O   ILE E 455 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 240 through 241
    Processing sheet with id=AC6, first strand: chain 'E' and resid 342 through 346
      removed outlier: 3.534A  pdb=" N   ASN E 345 " --> pdb=" O   PRO E 377 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 363 through 365
      removed outlier: 7.479A  pdb=" N   SER E 363 " --> pdb=" O   TYR E 416 " (cutoff:3.500A)
      removed outlier: 9.080A  pdb=" N   VAL E 418 " --> pdb=" O   SER E 363 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   ASP E 365 " --> pdb=" O   VAL E 418 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS E 417 " --> pdb=" O   LYS E 404 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL E 419 " --> pdb=" O   TYR E 402 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 461 through 464
      removed outlier: 6.240A  pdb=" N   LYS E 464 " --> pdb=" O   PHE E 492 " (cutoff:3.500A)
      removed outlier: 8.902A  pdb=" N   SER E 494 " --> pdb=" O   LYS E 464 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'E' and resid 466 through 467
      removed outlier: 3.501A  pdb=" N   GLU E 480 " --> pdb=" O   ASN E 467 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 637 through 640
      removed outlier: 6.725A  pdb=" N   LEU E 736 " --> pdb=" O   ILE E 748 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LYS E 744 " --> pdb=" O   GLN E 740 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 692 through 695
      removed outlier: 3.569A  pdb=" N   LEU E 713 " --> pdb=" O   TYR E 692 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 779 through 781
      removed outlier: 3.601A  pdb=" N   SER E 802 " --> pdb=" O   ARG E 814 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ARG E 814 " --> pdb=" O   SER E 802 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU E 804 " --> pdb=" O   PHE E 812 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'D' and resid 5 through 7
      removed outlier: 3.524A  pdb=" N   ASP D  18 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU D  15 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   THR D  37 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LYS D  35 " --> pdb=" O   GLU D  31 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE B  44 " --> pdb=" O   ILE F  53 " (cutoff:3.500A)
      removed outlier: 8.493A  pdb=" N   ASN F  55 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   SER B  46 " --> pdb=" O   ASN F  55 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER F  75 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER F  76 " --> pdb=" O   LYS F  87 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE F  86 " --> pdb=" O   ILE F  93 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE F  88 " --> pdb=" O   SER F  91 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 91 through 95
      removed outlier: 3.661A  pdb=" N   ILE B  88 " --> pdb=" O   SER B  91 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE B  86 " --> pdb=" O   ILE B  93 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER B  76 " --> pdb=" O   LYS B  87 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER B  75 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASN B  55 " --> pdb=" O   SER D  46 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LYS F  35 " --> pdb=" O   GLU F  31 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   THR F  37 " --> pdb=" O   LYS F  29 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU F  15 " --> pdb=" O   LEU F  30 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP F  18 " --> pdb=" O   ILE F   7 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 100 through 102
      removed outlier: 5.889A  pdb=" N   ILE B 100 " --> pdb=" O   ASN F 108 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   ASN D 116 " --> pdb=" O   ILE F 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'D' and resid 100 through 102
    Processing sheet with id=AD8, first strand: chain 'B' and resid 115 through 117
      removed outlier: 5.772A  pdb=" N   ASN B 116 " --> pdb=" O   ILE D 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD8
    Processing sheet with id=AD9, first strand: chain 'B' and resid 123 through 124
      removed outlier: 7.968A  pdb=" N   ILE B 123 " --> pdb=" O   ILE F 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD9

    522 hydrogen bonds defined for protein.
    1389 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.30

  Time building geometry restraints manager: 1.87 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: 6284
        1.34 -     1.46: 3013
        1.46 -     1.57: 10071
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 19413
  Sorted by residual:
  bond pdb=" CB  ASN A 387 "
       pdb=" CG  ASN A 387 "
    ideal  model  delta    sigma   weight residual
    1.516  1.456  0.060 2.50e-02 1.60e+03 5.80e+00
  bond pdb=" CB  ASN C 387 "
       pdb=" CG  ASN C 387 "
    ideal  model  delta    sigma   weight residual
    1.516  1.456  0.060 2.50e-02 1.60e+03 5.71e+00
  bond pdb=" CB  ASN E 387 "
       pdb=" CG  ASN E 387 "
    ideal  model  delta    sigma   weight residual
    1.516  1.457  0.059 2.50e-02 1.60e+03 5.60e+00
  bond pdb=" CA  ASN E 545 "
       pdb=" CB  ASN E 545 "
    ideal  model  delta    sigma   weight residual
    1.531  1.459  0.072 3.28e-02 9.30e+02 4.82e+00
  bond pdb=" CA  ASN C 545 "
       pdb=" CB  ASN C 545 "
    ideal  model  delta    sigma   weight residual
    1.531  1.460  0.071 3.28e-02 9.30e+02 4.63e+00
  ... (remaining 19408 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 24320
        1.92 -     3.84: 1575
        3.84 -     5.76: 229
        5.76 -     7.69: 55
        7.69 -     9.61: 35
  Bond angle restraints: 26214
  Sorted by residual:
  angle pdb=" N   PRO E  30 "
        pdb=" CA  PRO E  30 "
        pdb=" CB  PRO E  30 "
      ideal   model   delta    sigma   weight residual
     102.33  110.31   -7.98 1.18e+00 7.18e-01 4.58e+01
  angle pdb=" N   PRO A  30 "
        pdb=" CA  PRO A  30 "
        pdb=" CB  PRO A  30 "
      ideal   model   delta    sigma   weight residual
     102.33  110.29   -7.96 1.18e+00 7.18e-01 4.55e+01
  angle pdb=" N   PRO C  30 "
        pdb=" CA  PRO C  30 "
        pdb=" CB  PRO C  30 "
      ideal   model   delta    sigma   weight residual
     102.33  110.25   -7.92 1.18e+00 7.18e-01 4.51e+01
  angle pdb=" N   PRO C 128 "
        pdb=" CA  PRO C 128 "
        pdb=" CB  PRO C 128 "
      ideal   model   delta    sigma   weight residual
     103.44  110.01   -6.57 1.12e+00 7.97e-01 3.44e+01
  angle pdb=" N   PRO A 128 "
        pdb=" CA  PRO A 128 "
        pdb=" CB  PRO A 128 "
      ideal   model   delta    sigma   weight residual
     103.44  109.99   -6.55 1.12e+00 7.97e-01 3.42e+01
  ... (remaining 26209 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 11386
       16.06 -    32.12: 530
       32.12 -    48.18: 39
       48.18 -    64.24: 0
       64.24 -    80.30: 3
  Dihedral angle restraints: 11958
    sinusoidal: 4404
      harmonic: 7554
  Sorted by residual:
  dihedral pdb=" CA  PHE A 672 "
           pdb=" C   PHE A 672 "
           pdb=" N   GLN A 673 "
           pdb=" CA  GLN A 673 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.69   45.31     0      5.00e+00 4.00e-02 8.21e+01
  dihedral pdb=" CA  PHE C 672 "
           pdb=" C   PHE C 672 "
           pdb=" N   GLN C 673 "
           pdb=" CA  GLN C 673 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.71   45.29     0      5.00e+00 4.00e-02 8.21e+01
  dihedral pdb=" CA  PHE E 672 "
           pdb=" C   PHE E 672 "
           pdb=" N   GLN E 673 "
           pdb=" CA  GLN E 673 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.73   45.27     0      5.00e+00 4.00e-02 8.20e+01
  ... (remaining 11955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 2008
       0.052 -    0.104: 740
       0.104 -    0.155: 275
       0.155 -    0.207: 54
       0.207 -    0.259: 16
  Chirality restraints: 3093
  Sorted by residual:
  chirality pdb=" CB  ILE A 455 "
            pdb=" CA  ILE A 455 "
            pdb=" CG1 ILE A 455 "
            pdb=" CG2 ILE A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CB  ILE C 455 "
            pdb=" CA  ILE C 455 "
            pdb=" CG1 ILE C 455 "
            pdb=" CG2 ILE C 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  PRO E  30 "
            pdb=" N   PRO E  30 "
            pdb=" C   PRO E  30 "
            pdb=" CB  PRO E  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 3090 not shown)

  Planarity restraints: 3393
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 217 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.03e+00
        pdb=" C   LYS E 217 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LYS E 217 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN E 218 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 217 "    0.013 2.00e-02 2.50e+03   2.64e-02 6.95e+00
        pdb=" C   LYS A 217 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LYS A 217 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN A 218 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 217 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   LYS C 217 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS C 217 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASN C 218 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 3390 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1851
        2.73 -     3.28: 17258
        3.28 -     3.82: 29188
        3.82 -     4.36: 34093
        4.36 -     4.90: 57081
  Nonbonded interactions: 139471
  Sorted by model distance:
  nonbonded pdb=" O   SER B  98 "
            pdb=" OG1 THR F 106 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" OG1 THR D 106 "
            pdb=" O   SER F  98 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OD1 ASN B  39 "
            pdb=" OG  SER F  47 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" NH2 ARG A 730 "
            pdb=" OD1 ASN E 724 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   TYR C 505 "
            pdb=" OG  SER C 686 "
     model   vdw
     2.264 3.040
  ... (remaining 139466 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  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:             3.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.420
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
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      :  0.009   0.072  19413  Z= 0.387
  Angle     :  1.102   9.606  26214  Z= 0.603
  Chirality :  0.064   0.259   3093
  Planarity :  0.005   0.061   3393
  Dihedral  :  9.472  80.296   6984
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.43 %
    Favored  : 86.57 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.91 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.98 %

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: -4.71 (0.13), residues: 2472
  helix: -4.25 (0.10), residues: 420
  sheet: -2.06 (0.19), residues: 666
  loop : -3.42 (0.13), residues: 1386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 284 
 TYR   0.020   0.003   TYR E 627 
 PHE   0.027   0.004   PHE A 633 
 TRP   0.014   0.003   TRP E 334 
 HIS   0.014   0.003   HIS F   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00858 (19413)
  covalent geometry    : angle       1.10229 (26214)
  hydrogen bonds       : bond        0.30030 (  522)
  hydrogen bonds       : angle      10.66722 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  514 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 511
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8921 (mt) cc_final: 0.8279 (tt)
REVERT: A  182 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8621 (pt)
REVERT: A  185 ASN cc_start: 0.8740 (m-40) cc_final: 0.8089 (t0)
REVERT: A  268 ASP cc_start: 0.8135 (m-30) cc_final: 0.7703 (p0)
REVERT: A  299 ASP cc_start: 0.8317 (m-30) cc_final: 0.8103 (t0)
REVERT: A  326 PHE cc_start: 0.8889 (m-80) cc_final: 0.8560 (m-80)
REVERT: A  390 ASP cc_start: 0.9437 (m-30) cc_final: 0.9162 (m-30)
REVERT: A  438 LYS cc_start: 0.8507 (mttt) cc_final: 0.8002 (mmtt)
REVERT: A  506 ILE cc_start: 0.9400 (mt) cc_final: 0.9099 (tp)
REVERT: A  523 ILE cc_start: 0.9296 (mt) cc_final: 0.9014 (tt)
REVERT: A  529 ASN cc_start: 0.9041 (m-40) cc_final: 0.8665 (m-40)
REVERT: A  557 LYS cc_start: 0.7705 (mttt) cc_final: 0.7256 (mppt)
REVERT: A  568 PHE cc_start: 0.8268 (m-10) cc_final: 0.7967 (m-10)
REVERT: A  570 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.7624 (ptm160)
REVERT: A  653 LYS cc_start: 0.8641 (tttt) cc_final: 0.8005 (tppt)
REVERT: A  685 ASN cc_start: 0.8025 (m-40) cc_final: 0.7804 (t0)
REVERT: A  771 LEU cc_start: 0.8950 (mt) cc_final: 0.8685 (mm)
REVERT: A  778 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7659 (tt0)
REVERT: C  177 LEU cc_start: 0.8844 (mt) cc_final: 0.8175 (tt)
REVERT: C  185 ASN cc_start: 0.8763 (m-40) cc_final: 0.8094 (t0)
REVERT: C  228 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8005 (mt-10)
REVERT: C  263 ASP cc_start: 0.8241 (m-30) cc_final: 0.7853 (m-30)
REVERT: C  268 ASP cc_start: 0.8325 (m-30) cc_final: 0.7397 (p0)
REVERT: C  326 PHE cc_start: 0.9001 (m-80) cc_final: 0.8607 (m-80)
REVERT: C  438 LYS cc_start: 0.8681 (mttt) cc_final: 0.8085 (mttp)
REVERT: C  529 ASN cc_start: 0.9154 (m-40) cc_final: 0.8824 (m-40)
REVERT: C  550 LEU cc_start: 0.8948 (mt) cc_final: 0.8624 (pt)
REVERT: C  557 LYS cc_start: 0.7984 (mttt) cc_final: 0.7485 (mptt)
REVERT: C  574 CYS cc_start: 0.6303 (m) cc_final: 0.5870 (m)
REVERT: C  638 ILE cc_start: 0.9112 (mt) cc_final: 0.8491 (pt)
REVERT: C  653 LYS cc_start: 0.8439 (tttt) cc_final: 0.7861 (tppt)
REVERT: C  696 ILE cc_start: 0.7851 (mt) cc_final: 0.6759 (mm)
REVERT: C  771 LEU cc_start: 0.8831 (mt) cc_final: 0.8310 (mt)
REVERT: C  774 LYS cc_start: 0.8858 (tttt) cc_final: 0.8639 (ttmt)
REVERT: C  792 LEU cc_start: 0.8929 (mt) cc_final: 0.8546 (tt)
REVERT: E  177 LEU cc_start: 0.8665 (mt) cc_final: 0.8039 (tt)
REVERT: E  182 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8415 (pt)
REVERT: E  185 ASN cc_start: 0.8674 (m-40) cc_final: 0.7980 (t0)
REVERT: E  263 ASP cc_start: 0.8178 (m-30) cc_final: 0.7977 (m-30)
REVERT: E  268 ASP cc_start: 0.8202 (m-30) cc_final: 0.7563 (p0)
REVERT: E  326 PHE cc_start: 0.8886 (m-80) cc_final: 0.8316 (m-80)
REVERT: E  438 LYS cc_start: 0.8472 (mttt) cc_final: 0.7962 (mttp)
REVERT: E  506 ILE cc_start: 0.9410 (mt) cc_final: 0.9206 (tp)
REVERT: E  529 ASN cc_start: 0.8999 (m-40) cc_final: 0.8724 (m-40)
REVERT: E  550 LEU cc_start: 0.8997 (mt) cc_final: 0.8706 (pt)
REVERT: E  557 LYS cc_start: 0.7789 (mttt) cc_final: 0.7363 (mppt)
REVERT: E  566 LEU cc_start: 0.9125 (mt) cc_final: 0.8739 (mp)
REVERT: E  568 PHE cc_start: 0.8100 (m-10) cc_final: 0.7581 (m-10)
REVERT: E  570 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7529 (ptp-170)
REVERT: E  638 ILE cc_start: 0.9039 (mt) cc_final: 0.8793 (tp)
REVERT: E  653 LYS cc_start: 0.8570 (tttt) cc_final: 0.7976 (tppt)
REVERT: E  685 ASN cc_start: 0.8039 (m-40) cc_final: 0.7803 (t0)
REVERT: E  725 GLN cc_start: 0.8883 (mt0) cc_final: 0.8244 (mt0)
REVERT: E  771 LEU cc_start: 0.8843 (mt) cc_final: 0.8579 (mm)
REVERT: B   18 ASP cc_start: 0.8196 (p0) cc_final: 0.7899 (p0)
REVERT: B   31 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7383 (mp0)
REVERT: B   42 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7909 (mm-30)
REVERT: B   65 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8116 (tp30)
REVERT: B   78 MET cc_start: 0.8542 (ttt) cc_final: 0.8332 (ttt)
REVERT: B   90 ASN cc_start: 0.8035 (m-40) cc_final: 0.7653 (t0)
REVERT: D   26 CYS cc_start: 0.7770 (m) cc_final: 0.7206 (p)
REVERT: D   31 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7862 (mt-10)
REVERT: D   42 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7984 (mm-30)
REVERT: F   31 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7951 (mp0)
REVERT: F   78 MET cc_start: 0.8465 (ttt) cc_final: 0.8243 (ttt)
  outliers start: 3
  outliers final: 0
  residues processed: 511
  average time/residue: 0.1464
  time to fit residues: 111.7772
Evaluate side-chains
  256 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 254
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 216 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 194 optimal weight:    4.9990
   chunk 227 optimal weight:    0.7980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 247 optimal weight:    0.0980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 385 ASN
A 545 ASN
A 725 GLN
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 545 ASN
E 180 GLN
E 545 ASN
E 611 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.095696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.085744 restraints weight = 56885.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.087382 restraints weight = 34803.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.088539 restraints weight = 23727.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.089341 restraints weight = 17448.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.089935 restraints weight = 13617.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  19413  Z= 0.132
  Angle     :  0.688  10.684  26214  Z= 0.367
  Chirality :  0.050   0.180   3093
  Planarity :  0.004   0.038   3393
  Dihedral  :  7.398  36.513   2622
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.12 %

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: -3.94 (0.14), residues: 2472
  helix: -2.51 (0.17), residues: 447
  sheet: -1.59 (0.18), residues: 663
  loop : -3.30 (0.14), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 284 
 TYR   0.019   0.001   TYR A 579 
 PHE   0.019   0.002   PHE C 449 
 TRP   0.005   0.001   TRP E 236 
 HIS   0.004   0.001   HIS D   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (19413)
  covalent geometry    : angle       0.68791 (26214)
  hydrogen bonds       : bond        0.03565 (  522)
  hydrogen bonds       : angle       6.10719 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 371
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8421 (mt) cc_final: 0.8029 (tt)
REVERT: A  185 ASN cc_start: 0.8282 (m-40) cc_final: 0.8026 (t0)
REVERT: A  390 ASP cc_start: 0.9148 (m-30) cc_final: 0.8921 (m-30)
REVERT: A  516 ILE cc_start: 0.8531 (mt) cc_final: 0.7970 (mt)
REVERT: A  529 ASN cc_start: 0.8817 (m-40) cc_final: 0.8608 (m-40)
REVERT: A  569 LYS cc_start: 0.8239 (mmmm) cc_final: 0.8005 (mmmm)
REVERT: A  653 LYS cc_start: 0.8797 (tttt) cc_final: 0.8335 (tppt)
REVERT: A  775 GLU cc_start: 0.8353 (mp0) cc_final: 0.8023 (mp0)
REVERT: C  177 LEU cc_start: 0.8351 (mt) cc_final: 0.8028 (tt)
REVERT: C  185 ASN cc_start: 0.8503 (m-40) cc_final: 0.8187 (t0)
REVERT: C  230 ILE cc_start: 0.8782 (pt) cc_final: 0.8515 (pt)
REVERT: C  557 LYS cc_start: 0.7488 (mttt) cc_final: 0.7278 (mppt)
REVERT: C  574 CYS cc_start: 0.5712 (m) cc_final: 0.5410 (m)
REVERT: C  624 THR cc_start: 0.8608 (m) cc_final: 0.7937 (m)
REVERT: C  638 ILE cc_start: 0.9138 (mt) cc_final: 0.8839 (pt)
REVERT: C  653 LYS cc_start: 0.8605 (tttt) cc_final: 0.8277 (tppt)
REVERT: E  177 LEU cc_start: 0.8403 (mt) cc_final: 0.7934 (tt)
REVERT: E  185 ASN cc_start: 0.8439 (m-40) cc_final: 0.8076 (t0)
REVERT: E  230 ILE cc_start: 0.9100 (pt) cc_final: 0.8760 (pt)
REVERT: E  438 LYS cc_start: 0.8739 (mttt) cc_final: 0.8209 (mttp)
REVERT: E  516 ILE cc_start: 0.8495 (mt) cc_final: 0.7841 (mt)
REVERT: E  568 PHE cc_start: 0.7921 (m-10) cc_final: 0.7669 (m-10)
REVERT: E  624 THR cc_start: 0.8427 (m) cc_final: 0.8008 (m)
REVERT: E  653 LYS cc_start: 0.8733 (tttt) cc_final: 0.8306 (tppt)
REVERT: B    5 ASP cc_start: 0.8291 (m-30) cc_final: 0.7968 (m-30)
REVERT: B   69 LEU cc_start: 0.8267 (mp) cc_final: 0.8022 (tt)
REVERT: D    5 ASP cc_start: 0.8595 (m-30) cc_final: 0.8243 (m-30)
REVERT: F    5 ASP cc_start: 0.8293 (m-30) cc_final: 0.7959 (m-30)
REVERT: F   69 LEU cc_start: 0.8259 (mp) cc_final: 0.8043 (tt)
REVERT: F   90 ASN cc_start: 0.7425 (m110) cc_final: 0.7177 (t0)
REVERT: F  116 ASN cc_start: 0.7879 (m-40) cc_final: 0.6947 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 371
  average time/residue: 0.1262
  time to fit residues: 74.0867
Evaluate side-chains
  223 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 231 optimal weight:    0.8980
   chunk 106 optimal weight:    5.9990
   chunk 192 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 198 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 233 optimal weight:    0.9990
   chunk 140 optimal weight:    0.9980
   chunk 197 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN
A 725 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 GLN
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 ASN
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 718 ASN
E 378 GLN
E 611 ASN
** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 718 ASN
D 116 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.094986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.084417 restraints weight = 57645.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.086255 restraints weight = 34008.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.087495 restraints weight = 22590.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.088359 restraints weight = 16363.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.088969 restraints weight = 12658.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  19413  Z= 0.137
  Angle     :  0.643   9.467  26214  Z= 0.341
  Chirality :  0.049   0.175   3093
  Planarity :  0.003   0.037   3393
  Dihedral  :  6.710  36.765   2622
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.08 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.15), residues: 2472
  helix: -1.30 (0.21), residues: 450
  sheet: -1.17 (0.19), residues: 681
  loop : -3.23 (0.15), residues: 1341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 386 
 TYR   0.017   0.001   TYR E 579 
 PHE   0.016   0.001   PHE A 449 
 TRP   0.004   0.001   TRP E 236 
 HIS   0.004   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (19413)
  covalent geometry    : angle       0.64349 (26214)
  hydrogen bonds       : bond        0.03258 (  522)
  hydrogen bonds       : angle       5.31779 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 279
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8637 (mt) cc_final: 0.8209 (tt)
REVERT: A  390 ASP cc_start: 0.9188 (m-30) cc_final: 0.8841 (m-30)
REVERT: A  438 LYS cc_start: 0.8442 (mttp) cc_final: 0.8189 (mttp)
REVERT: A  516 ILE cc_start: 0.8469 (mt) cc_final: 0.7738 (mt)
REVERT: A  568 PHE cc_start: 0.8158 (m-80) cc_final: 0.7687 (m-10)
REVERT: A  569 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8021 (mmmm)
REVERT: A  653 LYS cc_start: 0.8830 (tttt) cc_final: 0.8306 (ttpt)
REVERT: A  775 GLU cc_start: 0.8479 (mp0) cc_final: 0.7876 (mp0)
REVERT: C  177 LEU cc_start: 0.8602 (mt) cc_final: 0.8158 (tt)
REVERT: C  185 ASN cc_start: 0.8557 (m-40) cc_final: 0.8202 (t0)
REVERT: C  230 ILE cc_start: 0.8865 (pt) cc_final: 0.8234 (pt)
REVERT: C  336 LYS cc_start: 0.8551 (mttt) cc_final: 0.8311 (mmtp)
REVERT: C  438 LYS cc_start: 0.8845 (mttt) cc_final: 0.8228 (mttp)
REVERT: C  626 GLU cc_start: 0.8211 (mp0) cc_final: 0.7814 (mp0)
REVERT: C  638 ILE cc_start: 0.9197 (mt) cc_final: 0.8757 (pt)
REVERT: C  653 LYS cc_start: 0.8628 (tttt) cc_final: 0.8286 (tppt)
REVERT: E  177 LEU cc_start: 0.8349 (mt) cc_final: 0.8065 (tt)
REVERT: E  185 ASN cc_start: 0.8568 (m-40) cc_final: 0.8180 (t0)
REVERT: E  230 ILE cc_start: 0.9168 (pt) cc_final: 0.8466 (pt)
REVERT: E  438 LYS cc_start: 0.8749 (mttt) cc_final: 0.8223 (mttp)
REVERT: E  516 ILE cc_start: 0.8563 (mt) cc_final: 0.8294 (tp)
REVERT: E  568 PHE cc_start: 0.8068 (m-10) cc_final: 0.7789 (m-10)
REVERT: E  626 GLU cc_start: 0.8032 (mp0) cc_final: 0.7737 (mp0)
REVERT: E  653 LYS cc_start: 0.8736 (tttt) cc_final: 0.8168 (tppt)
REVERT: B    5 ASP cc_start: 0.8315 (m-30) cc_final: 0.8038 (m-30)
REVERT: B   55 ASN cc_start: 0.8517 (t0) cc_final: 0.8247 (p0)
REVERT: D    5 ASP cc_start: 0.8519 (m-30) cc_final: 0.8272 (m-30)
REVERT: D   55 ASN cc_start: 0.8294 (t0) cc_final: 0.7948 (p0)
REVERT: F    5 ASP cc_start: 0.8382 (m-30) cc_final: 0.8034 (m-30)
REVERT: F  116 ASN cc_start: 0.7836 (m-40) cc_final: 0.7553 (m-40)
REVERT: F  124 ASP cc_start: 0.7979 (m-30) cc_final: 0.7512 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1247
  time to fit residues: 55.5645
Evaluate side-chains
  177 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 158 optimal weight:    0.0980
   chunk 93 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 79 optimal weight:   40.0000
   chunk 61 optimal weight:    3.9990
   chunk 223 optimal weight:    0.9990
   chunk 233 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 231 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 GLN
C 378 GLN
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 529 ASN
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 769 GLN
D 116 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.095194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.084521 restraints weight = 57204.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.086358 restraints weight = 33887.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.087578 restraints weight = 22555.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.088471 restraints weight = 16445.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.089061 restraints weight = 12699.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  19413  Z= 0.130
  Angle     :  0.622   9.079  26214  Z= 0.330
  Chirality :  0.048   0.175   3093
  Planarity :  0.003   0.037   3393
  Dihedral  :  6.316  35.961   2622
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.16), residues: 2472
  helix: -0.36 (0.24), residues: 432
  sheet: -0.98 (0.20), residues: 663
  loop : -3.03 (0.15), residues: 1377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 386 
 TYR   0.016   0.001   TYR C 579 
 PHE   0.012   0.001   PHE A 449 
 TRP   0.010   0.001   TRP A 334 
 HIS   0.004   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (19413)
  covalent geometry    : angle       0.62165 (26214)
  hydrogen bonds       : bond        0.02809 (  522)
  hydrogen bonds       : angle       4.88396 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8484 (mt) cc_final: 0.8052 (tt)
REVERT: A  390 ASP cc_start: 0.9177 (m-30) cc_final: 0.8805 (m-30)
REVERT: A  516 ILE cc_start: 0.8475 (mt) cc_final: 0.7704 (mt)
REVERT: A  568 PHE cc_start: 0.8139 (m-80) cc_final: 0.7550 (m-10)
REVERT: A  569 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8099 (mmmm)
REVERT: A  653 LYS cc_start: 0.8801 (tttt) cc_final: 0.8187 (ttpt)
REVERT: A  775 GLU cc_start: 0.8438 (mp0) cc_final: 0.7820 (mp0)
REVERT: C  177 LEU cc_start: 0.8525 (mt) cc_final: 0.8100 (tt)
REVERT: C  230 ILE cc_start: 0.8875 (pt) cc_final: 0.8411 (pt)
REVERT: C  438 LYS cc_start: 0.8892 (mttt) cc_final: 0.8246 (mttp)
REVERT: C  626 GLU cc_start: 0.8275 (mp0) cc_final: 0.7929 (mp0)
REVERT: C  653 LYS cc_start: 0.8747 (tttt) cc_final: 0.8337 (tppt)
REVERT: E  185 ASN cc_start: 0.8591 (m-40) cc_final: 0.8249 (t0)
REVERT: E  230 ILE cc_start: 0.9189 (pt) cc_final: 0.8577 (pt)
REVERT: E  438 LYS cc_start: 0.8794 (mttt) cc_final: 0.8221 (mttp)
REVERT: E  568 PHE cc_start: 0.8067 (m-10) cc_final: 0.7841 (m-10)
REVERT: E  626 GLU cc_start: 0.8130 (mp0) cc_final: 0.7818 (mp0)
REVERT: E  653 LYS cc_start: 0.8767 (tttt) cc_final: 0.8272 (tppt)
REVERT: B    5 ASP cc_start: 0.8209 (m-30) cc_final: 0.7901 (m-30)
REVERT: B   13 GLN cc_start: 0.8788 (mp10) cc_final: 0.7521 (mm-40)
REVERT: B   55 ASN cc_start: 0.8647 (t0) cc_final: 0.7722 (p0)
REVERT: D    5 ASP cc_start: 0.8457 (m-30) cc_final: 0.8205 (m-30)
REVERT: D   55 ASN cc_start: 0.8214 (t0) cc_final: 0.7903 (p0)
REVERT: F  116 ASN cc_start: 0.7812 (m-40) cc_final: 0.7550 (m-40)
REVERT: F  124 ASP cc_start: 0.7963 (m-30) cc_final: 0.7404 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 282
  average time/residue: 0.1257
  time to fit residues: 57.2111
Evaluate side-chains
  181 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 223 optimal weight:    1.9990
   chunk 149 optimal weight:   20.0000
   chunk 46 optimal weight:    4.9990
   chunk 216 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 154 optimal weight:    9.9990
   chunk 241 optimal weight:    2.9990
   chunk 183 optimal weight:    2.9990
   chunk 202 optimal weight:    0.0050
   overall best weight:    1.8002

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 429 ASN
C 611 ASN
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 769 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.092104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.082404 restraints weight = 58059.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.083923 restraints weight = 36169.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.084944 restraints weight = 25062.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.085626 restraints weight = 18813.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.086214 restraints weight = 15076.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  19413  Z= 0.200
  Angle     :  0.669   8.365  26214  Z= 0.359
  Chirality :  0.049   0.164   3093
  Planarity :  0.003   0.039   3393
  Dihedral  :  6.557  37.649   2622
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.20 %

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: -2.69 (0.16), residues: 2472
  helix:  0.07 (0.26), residues: 432
  sheet: -0.90 (0.20), residues: 663
  loop : -3.01 (0.15), residues: 1377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 386 
 TYR   0.021   0.001   TYR A 692 
 PHE   0.017   0.002   PHE C 636 
 TRP   0.008   0.001   TRP A 334 
 HIS   0.005   0.002   HIS F   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (19413)
  covalent geometry    : angle       0.66907 (26214)
  hydrogen bonds       : bond        0.03116 (  522)
  hydrogen bonds       : angle       5.04068 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ASP cc_start: 0.7101 (m-30) cc_final: 0.6809 (m-30)
REVERT: A  390 ASP cc_start: 0.9197 (m-30) cc_final: 0.8872 (m-30)
REVERT: A  568 PHE cc_start: 0.8379 (m-80) cc_final: 0.7582 (m-10)
REVERT: A  569 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8113 (mmmm)
REVERT: A  775 GLU cc_start: 0.8399 (mp0) cc_final: 0.7811 (mp0)
REVERT: C  438 LYS cc_start: 0.8903 (mttt) cc_final: 0.8321 (ttmt)
REVERT: C  568 PHE cc_start: 0.8316 (m-80) cc_final: 0.7977 (m-10)
REVERT: C  653 LYS cc_start: 0.8828 (tttt) cc_final: 0.8412 (ttpt)
REVERT: E  214 LEU cc_start: 0.8633 (tp) cc_final: 0.8394 (tt)
REVERT: E  230 ILE cc_start: 0.9199 (pt) cc_final: 0.8745 (pt)
REVERT: E  438 LYS cc_start: 0.8845 (mttt) cc_final: 0.8315 (ttmt)
REVERT: E  568 PHE cc_start: 0.8153 (m-10) cc_final: 0.7840 (m-10)
REVERT: E  626 GLU cc_start: 0.8150 (mp0) cc_final: 0.7802 (mp0)
REVERT: E  653 LYS cc_start: 0.8845 (tttt) cc_final: 0.8265 (tppt)
REVERT: B    5 ASP cc_start: 0.8272 (m-30) cc_final: 0.7971 (m-30)
REVERT: D    5 ASP cc_start: 0.8379 (m-30) cc_final: 0.8111 (m-30)
REVERT: D   55 ASN cc_start: 0.8385 (t0) cc_final: 0.7753 (p0)
REVERT: F  116 ASN cc_start: 0.8031 (m-40) cc_final: 0.7743 (m-40)
REVERT: F  124 ASP cc_start: 0.7964 (m-30) cc_final: 0.7435 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1177
  time to fit residues: 46.4687
Evaluate side-chains
  153 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 137 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9990
   chunk 226 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 246 optimal weight:    4.9990
   chunk 176 optimal weight:    5.9990
   chunk 230 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.093045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.083351 restraints weight = 58381.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.084887 restraints weight = 36908.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.085858 restraints weight = 25592.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.086653 restraints weight = 19321.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.087193 restraints weight = 15296.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  19413  Z= 0.157
  Angle     :  0.623   8.661  26214  Z= 0.332
  Chirality :  0.048   0.162   3093
  Planarity :  0.003   0.039   3393
  Dihedral  :  6.282  35.432   2622
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.32 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.17), residues: 2472
  helix:  0.41 (0.26), residues: 432
  sheet: -0.75 (0.21), residues: 681
  loop : -3.01 (0.15), residues: 1359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 386 
 TYR   0.022   0.001   TYR C 692 
 PHE   0.012   0.001   PHE C 636 
 TRP   0.007   0.001   TRP A 334 
 HIS   0.004   0.001   HIS C 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (19413)
  covalent geometry    : angle       0.62254 (26214)
  hydrogen bonds       : bond        0.02756 (  522)
  hydrogen bonds       : angle       4.80814 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8253 (mt) cc_final: 0.7476 (tt)
REVERT: A  263 ASP cc_start: 0.7078 (m-30) cc_final: 0.6804 (m-30)
REVERT: A  390 ASP cc_start: 0.9220 (m-30) cc_final: 0.8895 (m-30)
REVERT: A  568 PHE cc_start: 0.8244 (m-80) cc_final: 0.7760 (m-10)
REVERT: A  775 GLU cc_start: 0.8410 (mp0) cc_final: 0.7768 (mp0)
REVERT: C  438 LYS cc_start: 0.8959 (mttt) cc_final: 0.8383 (ttmt)
REVERT: C  568 PHE cc_start: 0.8357 (m-80) cc_final: 0.7909 (m-10)
REVERT: C  653 LYS cc_start: 0.8852 (tttt) cc_final: 0.8353 (ttpt)
REVERT: E  177 LEU cc_start: 0.8166 (mt) cc_final: 0.7902 (tt)
REVERT: E  214 LEU cc_start: 0.8541 (tp) cc_final: 0.8291 (tt)
REVERT: E  438 LYS cc_start: 0.8918 (mttt) cc_final: 0.8346 (ttmt)
REVERT: E  568 PHE cc_start: 0.8151 (m-10) cc_final: 0.7857 (m-10)
REVERT: E  653 LYS cc_start: 0.8806 (tttt) cc_final: 0.8321 (tppt)
REVERT: B    5 ASP cc_start: 0.8276 (m-30) cc_final: 0.7984 (m-30)
REVERT: B   13 GLN cc_start: 0.8737 (mp10) cc_final: 0.7346 (mm-40)
REVERT: D    5 ASP cc_start: 0.8382 (m-30) cc_final: 0.8045 (m-30)
REVERT: D   55 ASN cc_start: 0.8379 (t0) cc_final: 0.7748 (p0)
REVERT: F  122 ASN cc_start: 0.8108 (p0) cc_final: 0.7863 (p0)
REVERT: F  124 ASP cc_start: 0.7960 (m-30) cc_final: 0.7473 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1115
  time to fit residues: 42.9133
Evaluate side-chains
  155 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 129 optimal weight:    0.7980
   chunk 210 optimal weight:    2.9990
   chunk 206 optimal weight:    2.9990
   chunk 108 optimal weight:    0.2980
   chunk 45 optimal weight:    4.9990
   chunk 148 optimal weight:    9.9990
   chunk 224 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0570
   chunk 7 optimal weight:   30.0000
   chunk 247 optimal weight:    1.9990
   overall best weight:    1.0302

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

Flipped N/Q/H residues before XYZ refinement:
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.093885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.083295 restraints weight = 58151.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.085104 restraints weight = 34421.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.086362 restraints weight = 22949.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.087241 restraints weight = 16664.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.087884 restraints weight = 12875.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  19413  Z= 0.134
  Angle     :  0.605   8.875  26214  Z= 0.320
  Chirality :  0.048   0.176   3093
  Planarity :  0.003   0.036   3393
  Dihedral  :  6.017  33.828   2622
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.17), residues: 2472
  helix:  0.64 (0.27), residues: 432
  sheet: -0.73 (0.21), residues: 663
  loop : -2.95 (0.16), residues: 1377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 386 
 TYR   0.018   0.001   TYR E 692 
 PHE   0.016   0.001   PHE E 492 
 TRP   0.008   0.001   TRP A 334 
 HIS   0.004   0.001   HIS F   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (19413)
  covalent geometry    : angle       0.60505 (26214)
  hydrogen bonds       : bond        0.02575 (  522)
  hydrogen bonds       : angle       4.67475 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8374 (mt) cc_final: 0.7699 (tt)
REVERT: A  263 ASP cc_start: 0.7273 (m-30) cc_final: 0.7001 (m-30)
REVERT: A  268 ASP cc_start: 0.8026 (t0) cc_final: 0.7698 (p0)
REVERT: A  390 ASP cc_start: 0.9273 (m-30) cc_final: 0.8946 (m-30)
REVERT: A  568 PHE cc_start: 0.8418 (m-80) cc_final: 0.7835 (m-10)
REVERT: A  775 GLU cc_start: 0.8457 (mp0) cc_final: 0.7788 (mp0)
REVERT: C  438 LYS cc_start: 0.8988 (mttt) cc_final: 0.8418 (ttmt)
REVERT: C  568 PHE cc_start: 0.8331 (m-80) cc_final: 0.7824 (m-10)
REVERT: C  569 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8303 (mmmm)
REVERT: C  653 LYS cc_start: 0.8837 (tttt) cc_final: 0.8344 (ttpt)
REVERT: E  177 LEU cc_start: 0.8105 (mt) cc_final: 0.7744 (tt)
REVERT: E  263 ASP cc_start: 0.7281 (m-30) cc_final: 0.7067 (m-30)
REVERT: E  438 LYS cc_start: 0.8904 (mttt) cc_final: 0.8405 (ttmt)
REVERT: E  568 PHE cc_start: 0.8229 (m-10) cc_final: 0.7937 (m-10)
REVERT: E  653 LYS cc_start: 0.8878 (tttt) cc_final: 0.8166 (tppt)
REVERT: B    5 ASP cc_start: 0.8387 (m-30) cc_final: 0.8074 (m-30)
REVERT: B   13 GLN cc_start: 0.8763 (mp10) cc_final: 0.7558 (mm-40)
REVERT: D    5 ASP cc_start: 0.8422 (m-30) cc_final: 0.8095 (m-30)
REVERT: D   13 GLN cc_start: 0.8725 (mp10) cc_final: 0.7401 (mm-40)
REVERT: D   55 ASN cc_start: 0.8406 (t0) cc_final: 0.7800 (p0)
REVERT: F   13 GLN cc_start: 0.8669 (mp10) cc_final: 0.7399 (mm-40)
REVERT: F  116 ASN cc_start: 0.7934 (m-40) cc_final: 0.7695 (m-40)
REVERT: F  122 ASN cc_start: 0.8030 (p0) cc_final: 0.7790 (p0)
REVERT: F  124 ASP cc_start: 0.7829 (m-30) cc_final: 0.7338 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.1190
  time to fit residues: 48.4679
Evaluate side-chains
  167 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 228 optimal weight:    0.8980
   chunk 166 optimal weight:    0.8980
   chunk 152 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 150 optimal weight:    1.9990
   chunk 241 optimal weight:    8.9990
   chunk 187 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 156 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 769 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.094609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.084272 restraints weight = 57940.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.085998 restraints weight = 34918.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.087206 restraints weight = 23545.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.088041 restraints weight = 17226.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.088640 restraints weight = 13365.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.4696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  19413  Z= 0.120
  Angle     :  0.592   8.883  26214  Z= 0.314
  Chirality :  0.048   0.193   3093
  Planarity :  0.003   0.036   3393
  Dihedral  :  5.808  32.405   2622
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.12 %

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: -2.27 (0.17), residues: 2472
  helix:  0.89 (0.27), residues: 432
  sheet: -0.63 (0.21), residues: 666
  loop : -2.92 (0.16), residues: 1374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 386 
 TYR   0.016   0.001   TYR E 692 
 PHE   0.016   0.001   PHE A 392 
 TRP   0.006   0.001   TRP A 334 
 HIS   0.003   0.001   HIS C 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (19413)
  covalent geometry    : angle       0.59227 (26214)
  hydrogen bonds       : bond        0.02499 (  522)
  hydrogen bonds       : angle       4.54087 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8365 (mt) cc_final: 0.7775 (tt)
REVERT: A  268 ASP cc_start: 0.7985 (t0) cc_final: 0.7718 (p0)
REVERT: A  390 ASP cc_start: 0.9258 (m-30) cc_final: 0.8912 (m-30)
REVERT: A  482 ARG cc_start: 0.8641 (mtt180) cc_final: 0.7652 (mtt180)
REVERT: A  505 TYR cc_start: 0.8802 (p90) cc_final: 0.8060 (p90)
REVERT: A  568 PHE cc_start: 0.8193 (m-80) cc_final: 0.7696 (m-10)
REVERT: A  775 GLU cc_start: 0.8438 (mp0) cc_final: 0.7760 (mp0)
REVERT: C  390 ASP cc_start: 0.9256 (m-30) cc_final: 0.9014 (m-30)
REVERT: C  438 LYS cc_start: 0.8998 (mttt) cc_final: 0.8445 (ttmt)
REVERT: C  568 PHE cc_start: 0.8336 (m-80) cc_final: 0.7733 (m-10)
REVERT: C  569 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8275 (mmmm)
REVERT: E  177 LEU cc_start: 0.8086 (mt) cc_final: 0.7740 (tt)
REVERT: E  261 LEU cc_start: 0.8479 (tp) cc_final: 0.8138 (tp)
REVERT: E  263 ASP cc_start: 0.7355 (m-30) cc_final: 0.7069 (m-30)
REVERT: E  438 LYS cc_start: 0.8944 (mttt) cc_final: 0.8431 (ttmt)
REVERT: E  568 PHE cc_start: 0.8299 (m-10) cc_final: 0.8053 (m-10)
REVERT: E  653 LYS cc_start: 0.8874 (tttt) cc_final: 0.8260 (tppt)
REVERT: B    5 ASP cc_start: 0.8384 (m-30) cc_final: 0.8057 (m-30)
REVERT: B   13 GLN cc_start: 0.8759 (mp10) cc_final: 0.7513 (mm-40)
REVERT: D    5 ASP cc_start: 0.8393 (m-30) cc_final: 0.8043 (m-30)
REVERT: D   13 GLN cc_start: 0.8534 (mp10) cc_final: 0.7395 (mm-40)
REVERT: D   55 ASN cc_start: 0.8407 (t0) cc_final: 0.7827 (p0)
REVERT: F   13 GLN cc_start: 0.8629 (mp10) cc_final: 0.7434 (mm-40)
REVERT: F  116 ASN cc_start: 0.7787 (m-40) cc_final: 0.7504 (m-40)
REVERT: F  124 ASP cc_start: 0.7826 (m-30) cc_final: 0.7336 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1154
  time to fit residues: 45.5805
Evaluate side-chains
  169 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 195 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 240 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 245 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 116 optimal weight:    4.9990
   chunk 158 optimal weight:    7.9990
   chunk 209 optimal weight:    4.9990
   chunk 72 optimal weight:   20.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 GLN
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 769 GLN
D 116 ASN
F  51 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.087292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.077616 restraints weight = 60528.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079031 restraints weight = 38586.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080039 restraints weight = 27235.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.080745 restraints weight = 20676.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.081281 restraints weight = 16613.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.4621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061  19413  Z= 0.373
  Angle     :  0.879  10.935  26214  Z= 0.469
  Chirality :  0.054   0.207   3093
  Planarity :  0.005   0.046   3393
  Dihedral  :  7.457  40.284   2622
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.02 %
    Favored  : 83.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.12 %

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: -2.92 (0.16), residues: 2472
  helix:  0.01 (0.25), residues: 441
  sheet: -1.08 (0.21), residues: 648
  loop : -3.20 (0.15), residues: 1383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 482 
 TYR   0.029   0.002   TYR C 549 
 PHE   0.023   0.003   PHE C 803 
 TRP   0.009   0.002   TRP A 236 
 HIS   0.009   0.002   HIS C 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00825 (19413)
  covalent geometry    : angle       0.87944 (26214)
  hydrogen bonds       : bond        0.03880 (  522)
  hydrogen bonds       : angle       5.57529 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8502 (mt) cc_final: 0.7755 (tt)
REVERT: A  248 LYS cc_start: 0.5698 (mmtt) cc_final: 0.4739 (mttp)
REVERT: A  390 ASP cc_start: 0.9352 (m-30) cc_final: 0.9098 (m-30)
REVERT: A  775 GLU cc_start: 0.8312 (mp0) cc_final: 0.7600 (mp0)
REVERT: C  438 LYS cc_start: 0.9023 (mttt) cc_final: 0.8582 (mttp)
REVERT: C  569 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8021 (mmmm)
REVERT: C  570 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7794 (ptm160)
REVERT: E  330 LEU cc_start: 0.9519 (tp) cc_final: 0.9298 (tp)
REVERT: E  438 LYS cc_start: 0.9025 (mttt) cc_final: 0.8481 (mttp)
REVERT: E  568 PHE cc_start: 0.8399 (m-10) cc_final: 0.8098 (m-10)
REVERT: E  653 LYS cc_start: 0.8955 (tttt) cc_final: 0.8700 (ttmt)
REVERT: B   55 ASN cc_start: 0.8777 (t0) cc_final: 0.8540 (t0)
REVERT: D    5 ASP cc_start: 0.8195 (m-30) cc_final: 0.7788 (m-30)
REVERT: F  116 ASN cc_start: 0.8043 (m-40) cc_final: 0.7586 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1188
  time to fit residues: 39.0471
Evaluate side-chains
  143 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 228 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 145 optimal weight:   10.0000
   chunk 194 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 111 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0070
   chunk 172 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 685 ASN
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 685 ASN
D 116 ASN
F  13 GLN
F 121 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.093033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.082635 restraints weight = 58079.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.084427 restraints weight = 34338.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.085682 restraints weight = 22928.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.086546 restraints weight = 16606.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.087171 restraints weight = 12838.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  19413  Z= 0.125
  Angle     :  0.648   9.970  26214  Z= 0.342
  Chirality :  0.050   0.208   3093
  Planarity :  0.003   0.036   3393
  Dihedral  :  6.312  33.773   2622
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 5.26 %
    Twisted General : 0.20 %

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: -2.49 (0.17), residues: 2472
  helix:  0.75 (0.27), residues: 426
  sheet: -0.79 (0.21), residues: 660
  loop : -3.05 (0.15), residues: 1386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 386 
 TYR   0.019   0.001   TYR C 692 
 PHE   0.017   0.001   PHE A 392 
 TRP   0.007   0.001   TRP A 334 
 HIS   0.003   0.001   HIS F   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (19413)
  covalent geometry    : angle       0.64841 (26214)
  hydrogen bonds       : bond        0.02651 (  522)
  hydrogen bonds       : angle       4.80489 ( 1389)

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

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

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4944 Ramachandran restraints generated.
    2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 LEU cc_start: 0.8480 (mt) cc_final: 0.7731 (tt)
REVERT: A  248 LYS cc_start: 0.5679 (mmtt) cc_final: 0.4507 (tttm)
REVERT: A  294 ASN cc_start: 0.8704 (t0) cc_final: 0.8463 (t0)
REVERT: A  390 ASP cc_start: 0.9317 (m-30) cc_final: 0.9009 (m-30)
REVERT: A  438 LYS cc_start: 0.8842 (mttp) cc_final: 0.8607 (mttt)
REVERT: A  471 ASP cc_start: 0.7936 (m-30) cc_final: 0.7588 (m-30)
REVERT: A  568 PHE cc_start: 0.8342 (m-80) cc_final: 0.7917 (m-10)
REVERT: A  775 GLU cc_start: 0.8490 (mp0) cc_final: 0.7734 (mp0)
REVERT: C  438 LYS cc_start: 0.9022 (mttt) cc_final: 0.8392 (mttp)
REVERT: C  482 ARG cc_start: 0.8589 (mtt180) cc_final: 0.7821 (mtt180)
REVERT: C  499 ASN cc_start: 0.8545 (m110) cc_final: 0.8327 (m110)
REVERT: C  568 PHE cc_start: 0.8345 (m-80) cc_final: 0.7950 (m-10)
REVERT: C  569 LYS cc_start: 0.8329 (mmmm) cc_final: 0.8029 (mmmm)
REVERT: E  177 LEU cc_start: 0.8381 (mt) cc_final: 0.8028 (tt)
REVERT: E  261 LEU cc_start: 0.8509 (tp) cc_final: 0.8161 (tp)
REVERT: E  263 ASP cc_start: 0.7380 (m-30) cc_final: 0.7071 (m-30)
REVERT: E  438 LYS cc_start: 0.8963 (mttt) cc_final: 0.8429 (ttmt)
REVERT: E  568 PHE cc_start: 0.8281 (m-10) cc_final: 0.8013 (m-10)
REVERT: E  653 LYS cc_start: 0.8918 (tttt) cc_final: 0.8607 (ttmt)
REVERT: B   13 GLN cc_start: 0.8791 (mp10) cc_final: 0.7360 (mm-40)
REVERT: D    5 ASP cc_start: 0.8366 (m-30) cc_final: 0.8028 (m-30)
REVERT: D   13 GLN cc_start: 0.8698 (mp10) cc_final: 0.7340 (mm-40)
REVERT: F  116 ASN cc_start: 0.7841 (m-40) cc_final: 0.7406 (m-40)
REVERT: F  124 ASP cc_start: 0.7733 (m-30) cc_final: 0.7267 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1206
  time to fit residues: 47.2363
Evaluate side-chains
  167 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 186 optimal weight:    0.7980
   chunk 110 optimal weight:    0.0070
   chunk 220 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 229 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 146 optimal weight:    0.0670
   chunk 44 optimal weight:    5.9990
   chunk 145 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0770
   chunk 198 optimal weight:    8.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
A 685 ASN
A 769 GLN
** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 685 ASN
E 769 GLN
D 116 ASN
F 108 ASN
F 121 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.095749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.086041 restraints weight = 57370.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.087662 restraints weight = 35491.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.088766 restraints weight = 24240.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.089545 restraints weight = 17896.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.090071 restraints weight = 14058.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.5177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054  19413  Z= 0.102
  Angle     :  0.596  10.135  26214  Z= 0.313
  Chirality :  0.049   0.193   3093
  Planarity :  0.003   0.033   3393
  Dihedral  :  5.634  31.383   2622
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.86 %
    Twisted Proline : 1.75 %
    Twisted General : 0.12 %

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 (0.17), residues: 2472
  helix:  0.86 (0.26), residues: 447
  sheet: -0.53 (0.22), residues: 636
  loop : -3.01 (0.15), residues: 1389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 428 
 TYR   0.017   0.001   TYR C 692 
 PHE   0.018   0.001   PHE A 392 
 TRP   0.004   0.001   TRP C 334 
 HIS   0.004   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (19413)
  covalent geometry    : angle       0.59581 (26214)
  hydrogen bonds       : bond        0.02310 (  522)
  hydrogen bonds       : angle       4.45193 ( 1389)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2677.12 seconds
wall clock time: 47 minutes 40.31 seconds (2860.31 seconds total)