Starting phenix.real_space_refine
on Wed Sep 17 19:09:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cny_45766/09_2025/9cny_45766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cny_45766/09_2025/9cny_45766.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cny_45766/09_2025/9cny_45766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cny_45766/09_2025/9cny_45766.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cny_45766/09_2025/9cny_45766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cny_45766/09_2025/9cny_45766.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 235 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    6562      2.51       5
     N    1770      2.21       5
     O    2048      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10410
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5042
          Classifications: {'peptide': 634}
          Link IDs: {'PTRANS': 25, 'TRANS': 608}
    Chain: "C"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 363
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 6, 'TRANS': 45}
    Chain: "D"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1732
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 11, 'TRANS': 202}
    Chain: "E"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 685
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 81}
    Chain: "B"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2588
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 11, 'TRANS': 334}
          Chain breaks: 2
  Time building chain proxies: 2.64, per 1000 atoms: 0.25
  Number of scatterers: 10410
  At special positions: 0
  Unit cell: (102.153, 115.373, 139.409, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    2048      8.00
     N    1770      7.00
     C    6562      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.02

  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: 1.18
  Conformation dependent library (CDL) restraints added in 395.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      24.5% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 218 through 232
      removed outlier: 3.831A  pdb=" N   ASP A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.696A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 332
      No H-bonds generated for 'chain 'A' and resid 330 through 332'
    Processing helix  chain 'A' and resid 361 through 367
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.554A  pdb=" N   LYS A 386 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
    Processing helix  chain 'A' and resid 542 through 553
      removed outlier: 3.504A  pdb=" N   TRP A 546 " --> pdb=" O   GLN A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 730
    Processing helix  chain 'A' and resid 750 through 754
      removed outlier: 3.710A  pdb=" N   GLN A 753 " --> pdb=" O   ASP A 750 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 44
      removed outlier: 4.409A  pdb=" N   TYR C  41 " --> pdb=" O   ASP C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 66
      removed outlier: 3.963A  pdb=" N   TYR C  65 " --> pdb=" O   SER C  62 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA C  66 " --> pdb=" O   GLY C  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 62 through 66'
    Processing helix  chain 'C' and resid 76 through 80
      removed outlier: 3.568A  pdb=" N   ALA C  79 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 4.065A  pdb=" N   ALA D  57 " --> pdb=" O   THR D  53 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D  54 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASP D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASN D  60 " --> pdb=" O   GLU D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 97
    Processing helix  chain 'D' and resid 104 through 118
    Processing helix  chain 'D' and resid 119 through 121
      No H-bonds generated for 'chain 'D' and resid 119 through 121'
    Processing helix  chain 'D' and resid 123 through 129
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.512A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TYR D 177 " --> pdb=" O   ARG D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.735A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 3.686A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 44
      removed outlier: 3.586A  pdb=" N   SER E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 183
      removed outlier: 6.428A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLN A 179 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276
      removed outlier: 7.300A  pdb=" N   LEU A 337 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   VAL A 339 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 349
      removed outlier: 6.110A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 349
      removed outlier: 6.110A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLN A 403 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 430
      removed outlier: 6.107A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 738 " --> pdb=" O   GLY A 771 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A 771 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.846A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 6.541A  pdb=" N   THR E  90 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ASN E 106 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   THR E  92 " --> pdb=" O   ILE E 104 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   ILE E 104 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   THR E  94 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.724A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.873A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118
      removed outlier: 6.459A  pdb=" N   GLY B 114 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   TYR B 123 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   THR B 116 " --> pdb=" O   HIS B 121 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   HIS B 121 " --> pdb=" O   THR B 116 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   GLN B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.571A  pdb=" N   ALA B 173 " --> pdb=" O   TRP B 183 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASN B 175 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   VAL B 181 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 6.951A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 4.276A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.659A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 6.625A  pdb=" N   LEU B 346 " --> pdb=" O   GLN B 359 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   GLN B 359 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   TRP B 348 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)

    467 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 1.56 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: 3479
        1.34 -     1.46: 2170
        1.46 -     1.58: 4938
        1.58 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 10645
  Sorted by residual:
  bond pdb=" N   SER C  36 "
       pdb=" CA  SER C  36 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  bond pdb=" N   GLU E  24 "
       pdb=" CA  GLU E  24 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" N   ASP D  29 "
       pdb=" CA  ASP D  29 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" N   VAL A 173 "
       pdb=" CA  VAL A 173 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.83e+00
  bond pdb=" N   VAL B  30 "
       pdb=" CA  VAL B  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.74e+00
  ... (remaining 10640 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 14150
        1.77 -     3.54: 263
        3.54 -     5.30: 65
        5.30 -     7.07: 1
        7.07 -     8.84: 1
  Bond angle restraints: 14480
  Sorted by residual:
  angle pdb=" CB  MET B 189 "
        pdb=" CG  MET B 189 "
        pdb=" SD  MET B 189 "
      ideal   model   delta    sigma   weight residual
     112.70  121.54   -8.84 3.00e+00 1.11e-01 8.68e+00
  angle pdb=" C   GLY A 184 "
        pdb=" N   ASN A 185 "
        pdb=" CA  ASN A 185 "
      ideal   model   delta    sigma   weight residual
     121.54  126.53   -4.99 1.91e+00 2.74e-01 6.83e+00
  angle pdb=" CA  LYS B  31 "
        pdb=" CB  LYS B  31 "
        pdb=" CG  LYS B  31 "
      ideal   model   delta    sigma   weight residual
     114.10  119.05   -4.95 2.00e+00 2.50e-01 6.12e+00
  angle pdb=" N   VAL A 208 "
        pdb=" CA  VAL A 208 "
        pdb=" C   VAL A 208 "
      ideal   model   delta    sigma   weight residual
     113.71  111.40    2.31 9.50e-01 1.11e+00 5.93e+00
  angle pdb=" CA  ILE C  67 "
        pdb=" C   ILE C  67 "
        pdb=" N   PRO C  68 "
      ideal   model   delta    sigma   weight residual
     118.12  120.05   -1.93 8.10e-01 1.52e+00 5.65e+00
  ... (remaining 14475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5770
       17.98 -    35.96: 398
       35.96 -    53.94: 60
       53.94 -    71.93: 16
       71.93 -    89.91: 21
  Dihedral angle restraints: 6265
    sinusoidal: 2433
      harmonic: 3832
  Sorted by residual:
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.72   50.72     1      1.00e+01 1.00e-02 3.52e+01
  dihedral pdb=" CA  GLU B 127 "
           pdb=" C   GLU B 127 "
           pdb=" N   LYS B 128 "
           pdb=" CA  LYS B 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.62   24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ASN B 266 "
           pdb=" C   ASN B 266 "
           pdb=" N   LEU B 267 "
           pdb=" CA  LEU B 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.66   23.34     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 6262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 996
       0.033 -    0.066: 381
       0.066 -    0.100: 110
       0.100 -    0.133: 74
       0.133 -    0.166: 8
  Chirality restraints: 1569
  Sorted by residual:
  chirality pdb=" CA  TRP A 546 "
            pdb=" N   TRP A 546 "
            pdb=" C   TRP A 546 "
            pdb=" CB  TRP A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.90e-01
  chirality pdb=" CA  ILE B 296 "
            pdb=" N   ILE B 296 "
            pdb=" C   ILE B 296 "
            pdb=" CB  ILE B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CB  THR D  53 "
            pdb=" CA  THR D  53 "
            pdb=" OG1 THR D  53 "
            pdb=" CG2 THR D  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1566 not shown)

  Planarity restraints: 1911
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "    0.038 2.00e-02 2.50e+03   2.88e-02 2.07e+01
        pdb=" CG  TRP A 546 "   -0.078 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 586 "   -0.042 5.00e-02 4.00e+02   6.25e-02 6.24e+00
        pdb=" N   PRO A 587 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 587 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 587 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 227 "   -0.181 9.50e-02 1.11e+02   8.14e-02 4.42e+00
        pdb=" NE  ARG A 227 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 227 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 227 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 227 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1908 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 113
        2.58 -     3.16: 9190
        3.16 -     3.74: 15953
        3.74 -     4.32: 21581
        4.32 -     4.90: 36260
  Nonbonded interactions: 83097
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 548 "
            pdb=" OG  SER A 551 "
     model   vdw
     2.003 3.040
  nonbonded pdb=" OG  SER A 715 "
            pdb=" OD1 ASP A 740 "
     model   vdw
     2.049 3.040
  nonbonded pdb=" OG1 THR A 423 "
            pdb=" OE1 GLN A 446 "
     model   vdw
     2.065 3.040
  nonbonded pdb=" OD1 ASP B 363 "
            pdb=" OH  TYR B 388 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OD1 ASP A 362 "
            pdb=" NH1 ARG A 366 "
     model   vdw
     2.133 3.120
  ... (remaining 83092 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.910
  Find NCS groups from input model:        0.040
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
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      :  0.003   0.054  10646  Z= 0.156
  Angle     :  0.629   8.838  14482  Z= 0.336
  Chirality :  0.044   0.166   1569
  Planarity :  0.005   0.081   1911
  Dihedral  : 13.796  89.908   3830
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.23), residues: 1319
  helix:  0.43 (0.30), residues: 269
  sheet:  0.21 (0.26), residues: 387
  loop : -0.08 (0.25), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 227 
 TYR   0.023   0.002   TYR D 205 
 PHE   0.028   0.002   PHE A 197 
 TRP   0.078   0.002   TRP A 546 
 HIS   0.003   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10645)
  covalent geometry    : angle       0.62909 (14480)
  SS BOND              : bond        0.00881 (    1)
  SS BOND              : angle       1.97544 (    2)
  hydrogen bonds       : bond        0.20612 (  463)
  hydrogen bonds       : angle       8.27080 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.7678 (mmt) cc_final: 0.7062 (mmt)
REVERT: A  489 LEU cc_start: 0.8514 (mm) cc_final: 0.8290 (mm)
REVERT: A  711 MET cc_start: 0.8933 (ppp) cc_final: 0.8542 (ttp)
REVERT: C   78 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8041 (mmtt)
REVERT: D  134 ASP cc_start: 0.8335 (p0) cc_final: 0.8109 (p0)
REVERT: D  183 GLU cc_start: 0.8152 (tp30) cc_final: 0.7917 (tp30)
REVERT: E   41 ASN cc_start: 0.8794 (t0) cc_final: 0.8427 (p0)
REVERT: B   82 LYS cc_start: 0.7664 (mtpt) cc_final: 0.6980 (mtmt)
REVERT: B  223 GLN cc_start: 0.8066 (tt0) cc_final: 0.7682 (tm-30)
REVERT: B  266 ASN cc_start: 0.7176 (m110) cc_final: 0.6674 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1031
  time to fit residues: 32.8879
Evaluate side-chains
  165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0670
   overall best weight:    1.8122

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
A 390 ASN
A 538 ASN
A 573 ASN
A 606 ASN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN
B 301 GLN
B 334 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.141576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.110766 restraints weight = 19944.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.109827 restraints weight = 18062.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110889 restraints weight = 18029.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.111557 restraints weight = 13980.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.112025 restraints weight = 13125.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  10646  Z= 0.247
  Angle     :  0.674   7.920  14482  Z= 0.361
  Chirality :  0.047   0.178   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  5.295  26.742   1460
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.64 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.23), residues: 1319
  helix:  0.60 (0.31), residues: 279
  sheet: -0.09 (0.25), residues: 383
  loop : -0.22 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 173 
 TYR   0.022   0.002   TYR A 618 
 PHE   0.019   0.002   PHE A 197 
 TRP   0.064   0.003   TRP A 546 
 HIS   0.010   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (10645)
  covalent geometry    : angle       0.67445 (14480)
  SS BOND              : bond        0.00325 (    1)
  SS BOND              : angle       0.87566 (    2)
  hydrogen bonds       : bond        0.04644 (  463)
  hydrogen bonds       : angle       5.84433 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7917 (tp40) cc_final: 0.7209 (tm-30)
REVERT: A  369 MET cc_start: 0.7810 (mmt) cc_final: 0.7110 (mmt)
REVERT: A  483 VAL cc_start: 0.8764 (t) cc_final: 0.8384 (p)
REVERT: A  711 MET cc_start: 0.8851 (ppp) cc_final: 0.8313 (ttp)
REVERT: A  768 MET cc_start: 0.6613 (mtm) cc_final: 0.6316 (ttm)
REVERT: A  777 MET cc_start: 0.9288 (tpp) cc_final: 0.8669 (tpt)
REVERT: C   39 GLU cc_start: 0.8411 (mp0) cc_final: 0.7853 (mp0)
REVERT: C   78 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7996 (mmtt)
REVERT: D   42 LYS cc_start: 0.8366 (tptm) cc_final: 0.8138 (tptt)
REVERT: D  114 LEU cc_start: 0.8947 (mt) cc_final: 0.8200 (tp)
REVERT: D  134 ASP cc_start: 0.8621 (p0) cc_final: 0.8284 (p0)
REVERT: E   53 GLN cc_start: 0.7867 (tp40) cc_final: 0.7635 (tp40)
REVERT: B   82 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7432 (mtmt)
REVERT: B  168 ASN cc_start: 0.8107 (p0) cc_final: 0.7767 (p0)
REVERT: B  329 SER cc_start: 0.9452 (m) cc_final: 0.9201 (t)
  outliers start: 24
  outliers final: 15
  residues processed: 190
  average time/residue: 0.1093
  time to fit residues: 29.3137
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  301 GLN
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 91 optimal weight:    4.9990
   chunk 119 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 90 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.143723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.112163 restraints weight = 19828.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.111764 restraints weight = 16980.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.113212 restraints weight = 16082.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.113456 restraints weight = 12772.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.114273 restraints weight = 11687.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10646  Z= 0.152
  Angle     :  0.594   7.497  14482  Z= 0.313
  Chirality :  0.044   0.176   1569
  Planarity :  0.004   0.043   1911
  Dihedral  :  4.889  25.967   1460
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.51 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.23), residues: 1319
  helix:  0.80 (0.31), residues: 281
  sheet: -0.08 (0.25), residues: 380
  loop : -0.13 (0.25), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 391 
 TYR   0.018   0.002   TYR D 184 
 PHE   0.020   0.002   PHE A 197 
 TRP   0.027   0.002   TRP A 546 
 HIS   0.007   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10645)
  covalent geometry    : angle       0.59417 (14480)
  SS BOND              : bond        0.01486 (    1)
  SS BOND              : angle       0.51825 (    2)
  hydrogen bonds       : bond        0.03783 (  463)
  hydrogen bonds       : angle       5.36178 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 182
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7845 (tp40) cc_final: 0.7160 (tm-30)
REVERT: A  287 LEU cc_start: 0.8403 (mm) cc_final: 0.8169 (tp)
REVERT: A  413 ASP cc_start: 0.8140 (p0) cc_final: 0.7933 (p0)
REVERT: A  483 VAL cc_start: 0.8790 (t) cc_final: 0.8381 (p)
REVERT: A  617 THR cc_start: 0.9165 (m) cc_final: 0.8599 (p)
REVERT: A  646 MET cc_start: 0.7841 (tmm) cc_final: 0.7212 (tmm)
REVERT: A  711 MET cc_start: 0.8771 (ppp) cc_final: 0.8110 (ttp)
REVERT: A  768 MET cc_start: 0.6456 (mtm) cc_final: 0.6083 (ttm)
REVERT: A  777 MET cc_start: 0.9270 (tpp) cc_final: 0.8673 (tpt)
REVERT: C   39 GLU cc_start: 0.8421 (mp0) cc_final: 0.7982 (mp0)
REVERT: C   78 LYS cc_start: 0.8299 (mmtm) cc_final: 0.7950 (mmtt)
REVERT: D   42 LYS cc_start: 0.8282 (tptm) cc_final: 0.8002 (mmmt)
REVERT: D  134 ASP cc_start: 0.8554 (p0) cc_final: 0.8246 (p0)
REVERT: D  136 ASP cc_start: 0.8382 (m-30) cc_final: 0.7973 (m-30)
REVERT: D  187 GLU cc_start: 0.7764 (tt0) cc_final: 0.7480 (tm-30)
REVERT: D  188 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8633 (tpp80)
REVERT: D  207 ASP cc_start: 0.7791 (t70) cc_final: 0.7507 (t0)
REVERT: E   53 GLN cc_start: 0.7857 (tp40) cc_final: 0.7617 (tp40)
REVERT: E   87 THR cc_start: 0.9071 (t) cc_final: 0.8788 (p)
REVERT: B  168 ASN cc_start: 0.8034 (p0) cc_final: 0.7665 (p0)
REVERT: B  246 ASP cc_start: 0.8412 (p0) cc_final: 0.8020 (p0)
REVERT: B  280 LYS cc_start: 0.8465 (ptmm) cc_final: 0.8084 (ptmm)
  outliers start: 25
  outliers final: 19
  residues processed: 194
  average time/residue: 0.1071
  time to fit residues: 29.5723
Evaluate side-chains
  184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 121 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.3980
   chunk 97 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.141683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.110251 restraints weight = 19920.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.110214 restraints weight = 18224.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111114 restraints weight = 17857.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.111753 restraints weight = 14032.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112177 restraints weight = 13178.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10646  Z= 0.204
  Angle     :  0.605   6.656  14482  Z= 0.320
  Chirality :  0.044   0.166   1569
  Planarity :  0.004   0.046   1911
  Dihedral  :  4.867  26.324   1460
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.86 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.23), residues: 1319
  helix:  0.81 (0.31), residues: 280
  sheet: -0.18 (0.25), residues: 371
  loop : -0.28 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 391 
 TYR   0.027   0.002   TYR A 609 
 PHE   0.021   0.002   PHE A 197 
 TRP   0.019   0.002   TRP A 546 
 HIS   0.006   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (10645)
  covalent geometry    : angle       0.60477 (14480)
  SS BOND              : bond        0.00419 (    1)
  SS BOND              : angle       0.65919 (    2)
  hydrogen bonds       : bond        0.03801 (  463)
  hydrogen bonds       : angle       5.29408 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7906 (tp40) cc_final: 0.7195 (tm-30)
REVERT: A  287 LEU cc_start: 0.8429 (mm) cc_final: 0.8175 (tp)
REVERT: A  369 MET cc_start: 0.7803 (mmt) cc_final: 0.6937 (mmt)
REVERT: A  412 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8891 (p)
REVERT: A  413 ASP cc_start: 0.8238 (p0) cc_final: 0.7906 (p0)
REVERT: A  483 VAL cc_start: 0.8762 (t) cc_final: 0.8346 (p)
REVERT: A  617 THR cc_start: 0.9185 (m) cc_final: 0.8578 (p)
REVERT: A  711 MET cc_start: 0.8881 (ppp) cc_final: 0.8246 (ttp)
REVERT: A  768 MET cc_start: 0.6689 (mtm) cc_final: 0.6165 (ttm)
REVERT: C   39 GLU cc_start: 0.8505 (mp0) cc_final: 0.8065 (mp0)
REVERT: C   78 LYS cc_start: 0.8433 (mmtm) cc_final: 0.7974 (mmtt)
REVERT: D  134 ASP cc_start: 0.8669 (p0) cc_final: 0.8248 (p0)
REVERT: D  188 ARG cc_start: 0.8953 (tpp80) cc_final: 0.8738 (tpp80)
REVERT: E   87 THR cc_start: 0.9061 (t) cc_final: 0.8779 (p)
REVERT: B  168 ASN cc_start: 0.8246 (p0) cc_final: 0.7846 (p0)
REVERT: B  223 GLN cc_start: 0.7296 (tp40) cc_final: 0.7061 (tp-100)
REVERT: B  280 LYS cc_start: 0.8541 (ptmm) cc_final: 0.8288 (ptmm)
  outliers start: 31
  outliers final: 27
  residues processed: 194
  average time/residue: 0.1080
  time to fit residues: 29.7149
Evaluate side-chains
  192 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   66 ASP
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 14 optimal weight:    3.9990
   chunk 69 optimal weight:    0.4980
   chunk 127 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.139659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.108184 restraints weight = 20062.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.107950 restraints weight = 19335.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.108887 restraints weight = 18238.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.109544 restraints weight = 14558.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.109942 restraints weight = 13495.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10646  Z= 0.266
  Angle     :  0.646   6.851  14482  Z= 0.343
  Chirality :  0.045   0.157   1569
  Planarity :  0.004   0.049   1911
  Dihedral  :  5.008  26.898   1460
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.30 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.23), residues: 1319
  helix:  0.72 (0.31), residues: 280
  sheet: -0.22 (0.26), residues: 370
  loop : -0.29 (0.25), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 321 
 TYR   0.025   0.002   TYR A 609 
 PHE   0.021   0.002   PHE A 197 
 TRP   0.018   0.002   TRP A 546 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 (10645)
  covalent geometry    : angle       0.64568 (14480)
  SS BOND              : bond        0.00457 (    1)
  SS BOND              : angle       0.61921 (    2)
  hydrogen bonds       : bond        0.03951 (  463)
  hydrogen bonds       : angle       5.39661 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 166
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7930 (tp40) cc_final: 0.7276 (tm-30)
REVERT: A  369 MET cc_start: 0.7935 (mmt) cc_final: 0.7399 (mmt)
REVERT: A  412 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8892 (p)
REVERT: A  413 ASP cc_start: 0.8327 (p0) cc_final: 0.7981 (p0)
REVERT: A  617 THR cc_start: 0.9169 (m) cc_final: 0.8502 (p)
REVERT: A  711 MET cc_start: 0.8917 (ppp) cc_final: 0.8260 (ttp)
REVERT: A  768 MET cc_start: 0.6778 (mtm) cc_final: 0.6364 (ttm)
REVERT: C   39 GLU cc_start: 0.8711 (mp0) cc_final: 0.8472 (mp0)
REVERT: C   49 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7654 (tp30)
REVERT: C   78 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8294 (mmtt)
REVERT: D  134 ASP cc_start: 0.8784 (p0) cc_final: 0.8450 (p0)
REVERT: D  188 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8747 (tpp80)
REVERT: B  168 ASN cc_start: 0.8393 (p0) cc_final: 0.7995 (p0)
REVERT: B  223 GLN cc_start: 0.7231 (tp40) cc_final: 0.6917 (tp-100)
REVERT: B  231 ARG cc_start: 0.7616 (ttt180) cc_final: 0.7396 (ttt-90)
  outliers start: 45
  outliers final: 38
  residues processed: 192
  average time/residue: 0.1077
  time to fit residues: 29.2354
Evaluate side-chains
  195 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  564 SER
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   45 LYS
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 50 optimal weight:    0.4980
   chunk 114 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 47 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 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 = 0.3812 r_free = 0.3812 target = 0.144365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.110285 restraints weight = 19988.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.111948 restraints weight = 17381.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114002 restraints weight = 12859.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114028 restraints weight = 10431.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.114230 restraints weight = 10198.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10646  Z= 0.123
  Angle     :  0.569   8.385  14482  Z= 0.296
  Chirality :  0.043   0.160   1569
  Planarity :  0.004   0.038   1911
  Dihedral  :  4.613  25.257   1460
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.01 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.23), residues: 1319
  helix:  0.98 (0.32), residues: 276
  sheet: -0.21 (0.25), residues: 376
  loop : -0.10 (0.25), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 321 
 TYR   0.023   0.001   TYR A 585 
 PHE   0.021   0.001   PHE A 197 
 TRP   0.020   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10645)
  covalent geometry    : angle       0.56934 (14480)
  SS BOND              : bond        0.00173 (    1)
  SS BOND              : angle       0.74318 (    2)
  hydrogen bonds       : bond        0.03162 (  463)
  hydrogen bonds       : angle       5.00270 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 177
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7871 (tp40) cc_final: 0.7202 (tm-30)
REVERT: A  287 LEU cc_start: 0.8108 (tp) cc_final: 0.7510 (tp)
REVERT: A  412 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8920 (p)
REVERT: A  413 ASP cc_start: 0.8260 (p0) cc_final: 0.7967 (p0)
REVERT: A  483 VAL cc_start: 0.8657 (t) cc_final: 0.8297 (p)
REVERT: A  617 THR cc_start: 0.9162 (m) cc_final: 0.8579 (p)
REVERT: A  711 MET cc_start: 0.8838 (ppp) cc_final: 0.8081 (ttp)
REVERT: C   39 GLU cc_start: 0.8671 (mp0) cc_final: 0.8167 (mp0)
REVERT: C   49 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7501 (tp30)
REVERT: C   78 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8124 (mmtt)
REVERT: D  134 ASP cc_start: 0.8561 (p0) cc_final: 0.8133 (p0)
REVERT: D  188 ARG cc_start: 0.8825 (tpp80) cc_final: 0.8604 (tpp80)
REVERT: E   45 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8640 (ttpp)
REVERT: B   32 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8744 (ppp)
REVERT: B  168 ASN cc_start: 0.8135 (p0) cc_final: 0.7837 (p0)
REVERT: B  223 GLN cc_start: 0.7221 (tp40) cc_final: 0.6922 (tp-100)
REVERT: B  231 ARG cc_start: 0.7518 (ttt180) cc_final: 0.7220 (ttt-90)
REVERT: B  321 ASP cc_start: 0.8198 (m-30) cc_final: 0.7872 (m-30)
  outliers start: 33
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1081
  time to fit residues: 29.7454
Evaluate side-chains
  194 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue  237 ILE
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 47 optimal weight:    0.0170
   chunk 54 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 115 optimal weight:    0.3980
   chunk 23 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 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 = 0.3788 r_free = 0.3788 target = 0.137508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106144 restraints weight = 19710.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105840 restraints weight = 13257.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106881 restraints weight = 12656.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.107382 restraints weight = 11352.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107528 restraints weight = 10913.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10646  Z= 0.114
  Angle     :  0.574   7.281  14482  Z= 0.296
  Chirality :  0.043   0.169   1569
  Planarity :  0.004   0.042   1911
  Dihedral  :  4.499  24.427   1460
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.64 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.23), residues: 1319
  helix:  1.01 (0.32), residues: 276
  sheet: -0.12 (0.25), residues: 370
  loop : -0.09 (0.25), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 321 
 TYR   0.020   0.001   TYR A 585 
 PHE   0.019   0.001   PHE A 197 
 TRP   0.025   0.001   TRP B 317 
 HIS   0.002   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10645)
  covalent geometry    : angle       0.57370 (14480)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.89636 (    2)
  hydrogen bonds       : bond        0.03103 (  463)
  hydrogen bonds       : angle       4.83333 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7855 (tp40) cc_final: 0.7184 (tm-30)
REVERT: A  287 LEU cc_start: 0.8074 (tp) cc_final: 0.7542 (tp)
REVERT: A  383 ASP cc_start: 0.7632 (t0) cc_final: 0.7431 (m-30)
REVERT: A  412 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8789 (p)
REVERT: A  413 ASP cc_start: 0.8265 (p0) cc_final: 0.7922 (p0)
REVERT: A  617 THR cc_start: 0.9118 (m) cc_final: 0.8578 (p)
REVERT: A  650 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7379 (tm-30)
REVERT: A  711 MET cc_start: 0.8884 (ppp) cc_final: 0.8585 (ttp)
REVERT: A  738 PHE cc_start: 0.8712 (p90) cc_final: 0.8376 (p90)
REVERT: C   39 GLU cc_start: 0.8799 (mp0) cc_final: 0.8233 (mp0)
REVERT: C   49 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7557 (tp30)
REVERT: C   78 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8180 (mmtt)
REVERT: D  183 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7600 (tt0)
REVERT: B  168 ASN cc_start: 0.8239 (p0) cc_final: 0.7922 (p0)
REVERT: B  223 GLN cc_start: 0.7461 (tp40) cc_final: 0.7141 (tp-100)
  outliers start: 31
  outliers final: 26
  residues processed: 191
  average time/residue: 0.1044
  time to fit residues: 28.5317
Evaluate side-chains
  198 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  183 GLU
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 78 optimal weight:    0.4980
   chunk 120 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0470
   chunk 100 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5260

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

Flipped N/Q/H residues before XYZ refinement:
D  99 ASN
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  96 ASN
B 234 GLN
B 266 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.137737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106530 restraints weight = 19674.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107938 restraints weight = 16009.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109098 restraints weight = 13684.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109312 restraints weight = 11868.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.109506 restraints weight = 11561.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10646  Z= 0.117
  Angle     :  0.582   8.684  14482  Z= 0.299
  Chirality :  0.043   0.160   1569
  Planarity :  0.004   0.040   1911
  Dihedral  :  4.403  24.199   1460
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.27 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.23), residues: 1319
  helix:  0.99 (0.32), residues: 278
  sheet: -0.03 (0.25), residues: 370
  loop : -0.15 (0.25), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 321 
 TYR   0.022   0.001   TYR D 107 
 PHE   0.021   0.001   PHE A 197 
 TRP   0.025   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10645)
  covalent geometry    : angle       0.58207 (14480)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.93366 (    2)
  hydrogen bonds       : bond        0.03051 (  463)
  hydrogen bonds       : angle       4.75658 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7868 (tp40) cc_final: 0.7142 (tm-30)
REVERT: A  287 LEU cc_start: 0.8018 (tp) cc_final: 0.7357 (tp)
REVERT: A  413 ASP cc_start: 0.8264 (p0) cc_final: 0.7939 (p0)
REVERT: A  617 THR cc_start: 0.9110 (m) cc_final: 0.8636 (p)
REVERT: A  626 LYS cc_start: 0.8708 (mptt) cc_final: 0.8419 (mmtm)
REVERT: A  650 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7160 (tm-30)
REVERT: A  738 PHE cc_start: 0.8688 (p90) cc_final: 0.8392 (p90)
REVERT: C   39 GLU cc_start: 0.8743 (mp0) cc_final: 0.8221 (mp0)
REVERT: C   49 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7435 (tp30)
REVERT: C   78 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8156 (mmtt)
REVERT: D   99 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7662 (p0)
REVERT: D  134 ASP cc_start: 0.8582 (p0) cc_final: 0.8283 (p0)
REVERT: E   50 MET cc_start: 0.7548 (tpp) cc_final: 0.7192 (tpp)
REVERT: E   87 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8695 (p)
REVERT: B  221 MET cc_start: 0.8583 (mpp) cc_final: 0.8113 (mmp)
  outliers start: 34
  outliers final: 28
  residues processed: 190
  average time/residue: 0.1093
  time to fit residues: 29.4345
Evaluate side-chains
  199 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 169
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  183 GLU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 32 optimal weight:   30.0000
   chunk 87 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0270
   chunk 91 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.9042

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.136813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.105422 restraints weight = 19807.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107360 restraints weight = 16299.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.107706 restraints weight = 15072.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.108335 restraints weight = 12174.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108617 restraints weight = 10889.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10646  Z= 0.145
  Angle     :  0.597   9.473  14482  Z= 0.308
  Chirality :  0.043   0.156   1569
  Planarity :  0.004   0.041   1911
  Dihedral  :  4.437  22.369   1460
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.36 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.23), residues: 1319
  helix:  0.95 (0.32), residues: 277
  sheet: -0.01 (0.25), residues: 381
  loop : -0.12 (0.25), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 321 
 TYR   0.020   0.001   TYR D 107 
 PHE   0.021   0.001   PHE A 197 
 TRP   0.025   0.002   TRP B 317 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10645)
  covalent geometry    : angle       0.59740 (14480)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.83020 (    2)
  hydrogen bonds       : bond        0.03129 (  463)
  hydrogen bonds       : angle       4.77182 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 167
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7904 (tp40) cc_final: 0.7215 (tm-30)
REVERT: A  287 LEU cc_start: 0.8037 (tp) cc_final: 0.7364 (tp)
REVERT: A  413 ASP cc_start: 0.8266 (p0) cc_final: 0.7936 (p0)
REVERT: A  617 THR cc_start: 0.9133 (m) cc_final: 0.8596 (p)
REVERT: A  626 LYS cc_start: 0.8740 (mptt) cc_final: 0.8464 (mmtm)
REVERT: A  650 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7149 (tm-30)
REVERT: A  711 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8351 (ttp)
REVERT: A  738 PHE cc_start: 0.8756 (p90) cc_final: 0.8417 (p90)
REVERT: C   39 GLU cc_start: 0.8762 (mp0) cc_final: 0.8247 (mp0)
REVERT: C   49 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7500 (tp30)
REVERT: C   78 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8134 (mmtt)
REVERT: E   50 MET cc_start: 0.7514 (tpp) cc_final: 0.7177 (tpp)
  outliers start: 38
  outliers final: 31
  residues processed: 184
  average time/residue: 0.1040
  time to fit residues: 27.4257
Evaluate side-chains
  196 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain B residue   32 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 97 optimal weight:    0.0980
   chunk 49 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 111 optimal weight:    2.9990
   chunk 32 optimal weight:   30.0000
   chunk 121 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 68 optimal weight:    0.0770
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 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 = 0.3799 r_free = 0.3799 target = 0.138528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106776 restraints weight = 19643.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.108135 restraints weight = 16468.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109037 restraints weight = 14422.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.109553 restraints weight = 12105.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109753 restraints weight = 11390.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10646  Z= 0.111
  Angle     :  0.595   9.422  14482  Z= 0.305
  Chirality :  0.043   0.155   1569
  Planarity :  0.004   0.040   1911
  Dihedral  :  4.315  22.249   1460
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.90 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.23), residues: 1319
  helix:  1.05 (0.32), residues: 276
  sheet:  0.01 (0.25), residues: 390
  loop : -0.03 (0.26), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 321 
 TYR   0.018   0.001   TYR D 107 
 PHE   0.020   0.001   PHE A 197 
 TRP   0.028   0.001   TRP B 317 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10645)
  covalent geometry    : angle       0.59497 (14480)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.97644 (    2)
  hydrogen bonds       : bond        0.02893 (  463)
  hydrogen bonds       : angle       4.64899 ( 1278)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7922 (tp40) cc_final: 0.7512 (tm-30)
REVERT: A  287 LEU cc_start: 0.7990 (tp) cc_final: 0.7697 (tp)
REVERT: A  413 ASP cc_start: 0.8219 (p0) cc_final: 0.7897 (p0)
REVERT: A  617 THR cc_start: 0.9218 (m) cc_final: 0.8762 (p)
REVERT: A  626 LYS cc_start: 0.8709 (mptt) cc_final: 0.8440 (mmtm)
REVERT: A  711 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8348 (ttp)
REVERT: C   39 GLU cc_start: 0.8713 (mp0) cc_final: 0.8212 (mp0)
REVERT: C   78 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8050 (mmtt)
REVERT: E   50 MET cc_start: 0.7643 (tpp) cc_final: 0.7235 (tpp)
REVERT: E   87 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8688 (p)
REVERT: B  188 ASP cc_start: 0.7725 (t0) cc_final: 0.7482 (m-30)
REVERT: B  221 MET cc_start: 0.8617 (mpp) cc_final: 0.8109 (mmp)
REVERT: B  246 ASP cc_start: 0.8316 (p0) cc_final: 0.8072 (p0)
  outliers start: 31
  outliers final: 28
  residues processed: 187
  average time/residue: 0.1036
  time to fit residues: 28.1443
Evaluate side-chains
  196 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  538 ASN
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   68 SER
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   45 LYS
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  349 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 100 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 81 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0870
   overall best weight:    0.6562

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.137580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.105386 restraints weight = 19835.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.107367 restraints weight = 18105.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.108097 restraints weight = 13826.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.108644 restraints weight = 12012.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109172 restraints weight = 10810.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10646  Z= 0.125
  Angle     :  0.593   9.270  14482  Z= 0.304
  Chirality :  0.043   0.153   1569
  Planarity :  0.004   0.040   1911
  Dihedral  :  4.295  21.840   1460
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.26 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.23), residues: 1319
  helix:  1.09 (0.32), residues: 273
  sheet:  0.05 (0.25), residues: 396
  loop : -0.05 (0.26), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 321 
 TYR   0.017   0.001   TYR A 585 
 PHE   0.020   0.001   PHE A 197 
 TRP   0.027   0.001   TRP B 317 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10645)
  covalent geometry    : angle       0.59313 (14480)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       0.96612 (    2)
  hydrogen bonds       : bond        0.03010 (  463)
  hydrogen bonds       : angle       4.64728 ( 1278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1725.26 seconds
wall clock time: 30 minutes 51.17 seconds (1851.17 seconds total)