Starting phenix.real_space_refine
on Wed Feb  4 05:22:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zv1_60504/02_2026/8zv1_60504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zv1_60504/02_2026/8zv1_60504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zv1_60504/02_2026/8zv1_60504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zv1_60504/02_2026/8zv1_60504.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zv1_60504/02_2026/8zv1_60504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zv1_60504/02_2026/8zv1_60504.map"
  }
  resolution = 2.8
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      50      5.16       5
     C    5468      2.51       5
     N    1515      2.21       5
     O    1655      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8692
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 673, 5190
          Classifications: {'peptide': 673}
          Link IDs: {'PTRANS': 24, 'TRANS': 648}
    Chain: "B"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1713
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 206}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1738
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 51
          Unusual residues: {' MG': 1, 'ATP': 1, 'BCT': 1, 'BTN': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'BTN:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.71, per 1000 atoms: 0.20
  Number of scatterers: 8692
  At special positions: 0
  Unit cell: (94.92, 98.28, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      50     16.00
     P       3     15.00
     Mg      1     11.99
     O    1655      8.00
     N    1515      7.00
     C    5468      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 214.3 milliseconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 13 sheets defined
      37.2% alpha, 23.8% 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 72 through 85
    Processing helix  chain 'A' and resid 100 through 106
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 123 through 135
      removed outlier: 3.539A  pdb=" N   ILE A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.533A  pdb=" N   GLU A 159 " --> pdb=" O   CYS A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 174
    Processing helix  chain 'A' and resid 177 through 187
    Processing helix  chain 'A' and resid 201 through 213
    Processing helix  chain 'A' and resid 234 through 252
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 4.367A  pdb=" N   THR A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU A 362 " --> pdb=" O   HIS A 358 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 364 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'A' and resid 458 through 472
    Processing helix  chain 'A' and resid 481 through 490
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 502 through 508
    Processing helix  chain 'A' and resid 518 through 540
    Processing helix  chain 'A' and resid 641 through 648
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.978A  pdb=" N   ILE B 319 " --> pdb=" O   ASN B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 328
    Processing helix  chain 'B' and resid 361 through 365
    Processing helix  chain 'B' and resid 367 through 384
    Processing helix  chain 'B' and resid 400 through 406
    Processing helix  chain 'B' and resid 407 through 422
      removed outlier: 3.890A  pdb=" N   ALA B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 442
      removed outlier: 4.218A  pdb=" N   ASP B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET B 442 " --> pdb=" O   ALA B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
      removed outlier: 3.613A  pdb=" N   CYS B 448 " --> pdb=" O   LYS B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 499
    Processing helix  chain 'B' and resid 507 through 509
      No H-bonds generated for 'chain 'B' and resid 507 through 509'
    Processing helix  chain 'B' and resid 510 through 523
    Processing helix  chain 'F' and resid 52 through 61
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 134 through 152
      removed outlier: 4.065A  pdb=" N   ALA F 138 " --> pdb=" O   SER F 134 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 172 through 187
    Processing helix  chain 'F' and resid 201 through 204
      removed outlier: 3.923A  pdb=" N   ALA F 204 " --> pdb=" O   ALA F 201 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 201 through 204'
    Processing helix  chain 'F' and resid 205 through 211
      removed outlier: 3.804A  pdb=" N   ALA F 209 " --> pdb=" O   VAL F 205 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 227 through 236
    Processing helix  chain 'F' and resid 240 through 246
    Processing helix  chain 'F' and resid 246 through 253
    Processing helix  chain 'F' and resid 263 through 276
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 3.531A  pdb=" N   VAL A 110 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ILE A  66 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   ILE A  92 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   VAL A  68 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ALA A 138 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232
    Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 289
      removed outlier: 4.076A  pdb=" N   GLN A 273 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   GLU A 287 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   GLU A 271 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   GLU A 289 " --> pdb=" O   HIS A 269 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   HIS A 269 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 294
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 416
      removed outlier: 3.562A  pdb=" N   GLY A 415 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 421
    Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 565
      removed outlier: 6.536A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR A 632 " --> pdb=" O   PHE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 663
      removed outlier: 3.830A  pdb=" N   LEU A 662 " --> pdb=" O   VAL A 725 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL A 725 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER A 709 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY A 705 " --> pdb=" O   VAL A 681 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 695 through 700
      removed outlier: 6.858A  pdb=" N   MET A 695 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLU A 691 " --> pdb=" O   MET A 695 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ASN A 697 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   VAL A 689 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   ILE A 687 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   VAL A 673 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.580A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.859A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   GLU B 459 " --> pdb=" O   ILE B 430 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ARG B 432 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ALA B 461 " --> pdb=" O   ARG B 432 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ALA B 434 " --> pdb=" O   ALA B 461 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.580A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.859A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 451 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 82
      removed outlier: 4.720A  pdb=" N   THR F 109 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 8.579A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ARG F 259 " --> pdb=" O   THR F 214 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1125 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1482
        1.32 -     1.44: 2206
        1.44 -     1.57: 5075
        1.57 -     1.69: 8
        1.69 -     1.81: 80
  Bond restraints: 8851
  Sorted by residual:
  bond pdb=" C2  BTN A 801 "
       pdb=" S1  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.824  1.436  0.388 2.00e-02 2.50e+03 3.77e+02
  bond pdb=" C3  BTN A 801 "
       pdb=" N2  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.362  1.556 -0.194 2.00e-02 2.50e+03 9.42e+01
  bond pdb=" C3  BTN A 801 "
       pdb=" N1  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.358  1.508 -0.150 2.00e-02 2.50e+03 5.61e+01
  bond pdb=" C2  BTN A 801 "
       pdb=" C4  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.534  1.682 -0.148 2.00e-02 2.50e+03 5.50e+01
  bond pdb=" C2  BTN A 801 "
       pdb=" C7  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.517  1.636 -0.119 2.00e-02 2.50e+03 3.55e+01
  ... (remaining 8846 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 11941
        3.28 -     6.56: 39
        6.56 -     9.84: 1
        9.84 -    13.12: 0
       13.12 -    16.40: 1
  Bond angle restraints: 11982
  Sorted by residual:
  angle pdb=" C2  BTN A 801 "
        pdb=" S1  BTN A 801 "
        pdb=" C6  BTN A 801 "
      ideal   model   delta    sigma   weight residual
      88.98  105.38  -16.40 3.00e+00 1.11e-01 2.99e+01
  angle pdb=" C   SER A 659 "
        pdb=" CA  SER A 659 "
        pdb=" CB  SER A 659 "
      ideal   model   delta    sigma   weight residual
     116.54  110.42    6.12 1.15e+00 7.56e-01 2.83e+01
  angle pdb=" CA  SER A 659 "
        pdb=" C   SER A 659 "
        pdb=" N   SER A 660 "
      ideal   model   delta    sigma   weight residual
     119.52  116.79    2.73 7.90e-01 1.60e+00 1.19e+01
  angle pdb=" N   GLU A 248 "
        pdb=" CA  GLU A 248 "
        pdb=" CB  GLU A 248 "
      ideal   model   delta    sigma   weight residual
     110.28  114.56   -4.28 1.55e+00 4.16e-01 7.62e+00
  angle pdb=" C   ALA B 420 "
        pdb=" N   GLU B 421 "
        pdb=" CA  GLU B 421 "
      ideal   model   delta    sigma   weight residual
     121.58  116.86    4.72 1.95e+00 2.63e-01 5.85e+00
  ... (remaining 11977 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 4919
       16.55 -    33.10: 351
       33.10 -    49.65: 76
       49.65 -    66.20: 26
       66.20 -    82.75: 12
  Dihedral angle restraints: 5384
    sinusoidal: 2162
      harmonic: 3222
  Sorted by residual:
  dihedral pdb=" CA  MET A 666 "
           pdb=" C   MET A 666 "
           pdb=" N   PRO A 667 "
           pdb=" CA  PRO A 667 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.92   23.08     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  ARG B 432 "
           pdb=" C   ARG B 432 "
           pdb=" N   LYS B 433 "
           pdb=" CA  LYS B 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.44  -15.56     0      5.00e+00 4.00e-02 9.69e+00
  dihedral pdb=" C6  BTN A 801 "
           pdb=" C2  BTN A 801 "
           pdb=" S1  BTN A 801 "
           pdb=" C7  BTN A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     169.29   86.54   82.75     1      3.00e+01 1.11e-03 9.32e+00
  ... (remaining 5381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 975
       0.041 -    0.082: 258
       0.082 -    0.123: 120
       0.123 -    0.164: 7
       0.164 -    0.205: 1
  Chirality restraints: 1361
  Sorted by residual:
  chirality pdb=" CB  VAL A 112 "
            pdb=" CA  VAL A 112 "
            pdb=" CG1 VAL A 112 "
            pdb=" CG2 VAL A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  GLU A 211 "
            pdb=" N   GLU A 211 "
            pdb=" C   GLU A 211 "
            pdb=" CB  GLU A 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" CA  ILE A 192 "
            pdb=" N   ILE A 192 "
            pdb=" C   ILE A 192 "
            pdb=" CB  ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 1358 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 301 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" CD  GLU A 301 "    0.027 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 301 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 301 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 446 "   -0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO A 447 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 447 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 447 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 494 "    0.022 5.00e-02 4.00e+02   3.27e-02 1.71e+00
        pdb=" N   PRO B 495 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 495 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 495 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 117
        2.65 -     3.21: 7890
        3.21 -     3.77: 13153
        3.77 -     4.34: 18310
        4.34 -     4.90: 30399
  Nonbonded interactions: 69869
  Sorted by model distance:
  nonbonded pdb=" O2G ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.083 2.170
  nonbonded pdb=" OD1 ASP A 309 "
            pdb=" OG1 THR A 312 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O1A ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.224 2.170
  nonbonded pdb=" O   ALA F 247 "
            pdb=" OG1 THR F 251 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   GLY A 280 "
            pdb=" NH1 ARG A 325 "
     model   vdw
     2.319 3.120
  ... (remaining 69864 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 individual isotropic
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:                  0.010
  Normalize map: mean=0, sd=1:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.430
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.388   8852  Z= 0.339
  Angle     :  0.571  16.403  11982  Z= 0.295
  Chirality :  0.044   0.205   1361
  Planarity :  0.003   0.044   1556
  Dihedral  : 13.170  82.750   3310
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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 are not related in a simple way.
  whole:  0.63 (0.26), residues: 1115
  helix:  1.47 (0.27), residues: 382
  sheet:  0.81 (0.35), residues: 232
  loop : -0.57 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 257 
 TYR   0.016   0.001   TYR A 473 
 PHE   0.008   0.001   PHE A 503 
 TRP   0.019   0.001   TRP A 394 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 8851)
  covalent geometry    : angle       0.57115 (11982)
  hydrogen bonds       : bond        0.13430 (  383)
  hydrogen bonds       : angle       5.69569 ( 1125)
  Misc. bond           : bond        0.13050 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  392 ASN cc_start: 0.8326 (t0) cc_final: 0.8008 (t0)
REVERT: B  503 ASP cc_start: 0.7655 (m-30) cc_final: 0.7349 (m-30)
REVERT: F   58 GLN cc_start: 0.7638 (tp40) cc_final: 0.7355 (tp40)
REVERT: F   61 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.7887 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.5771
  time to fit residues: 76.4524
Evaluate side-chains
  89 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0060
   chunk 65 optimal weight:   40.0000
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0570
   overall best weight:    0.5514

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.142275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091003 restraints weight = 15989.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 3.62
r_work: 0.3089 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8852  Z= 0.113
  Angle     :  0.554  11.407  11982  Z= 0.281
  Chirality :  0.045   0.238   1361
  Planarity :  0.003   0.034   1556
  Dihedral  :  7.027  61.071   1264
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  7.36 %
    Favored  : 91.36 %
  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 are not related in a simple way.
  whole:  0.60 (0.26), residues: 1115
  helix:  1.34 (0.26), residues: 402
  sheet:  1.02 (0.36), residues: 218
  loop : -0.66 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  77 
 TYR   0.015   0.001   TYR A 473 
 PHE   0.025   0.001   PHE A 345 
 TRP   0.006   0.001   TRP A 394 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8851)
  covalent geometry    : angle       0.55429 (11982)
  hydrogen bonds       : bond        0.03803 (  383)
  hydrogen bonds       : angle       4.75690 ( 1125)
  Misc. bond           : bond        0.00031 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 PHE cc_start: 0.8576 (p90) cc_final: 0.8368 (p90)
REVERT: A  392 ASN cc_start: 0.8743 (t0) cc_final: 0.8350 (t0)
REVERT: F   58 GLN cc_start: 0.7447 (tp40) cc_final: 0.7038 (tp40)
REVERT: F   61 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.7704 (mtm-85)
REVERT: F   84 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6351 (tpp)
  outliers start: 12
  outliers final: 3
  residues processed: 110
  average time/residue: 0.5680
  time to fit residues: 66.4762
Evaluate side-chains
  92 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  442 MET
Chi-restraints excluded: chain F residue   84 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 65 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 103 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 528 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.141180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.089945 restraints weight = 15753.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 3.41
r_work: 0.3064 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8852  Z= 0.121
  Angle     :  0.524  11.712  11982  Z= 0.265
  Chirality :  0.045   0.252   1361
  Planarity :  0.003   0.031   1556
  Dihedral  :  5.990  55.776   1264
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.45 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1115
  helix:  1.39 (0.27), residues: 396
  sheet:  1.11 (0.36), residues: 208
  loop : -0.75 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 465 
 TYR   0.015   0.001   TYR A 473 
 PHE   0.020   0.001   PHE A 345 
 TRP   0.013   0.001   TRP A 233 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8851)
  covalent geometry    : angle       0.52410 (11982)
  hydrogen bonds       : bond        0.03814 (  383)
  hydrogen bonds       : angle       4.56068 ( 1125)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 PHE cc_start: 0.8613 (p90) cc_final: 0.8407 (p90)
REVERT: A  392 ASN cc_start: 0.8754 (t0) cc_final: 0.8317 (t0)
REVERT: F   58 GLN cc_start: 0.7384 (tp40) cc_final: 0.7031 (tp40)
REVERT: F   61 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.7750 (mtm-85)
REVERT: F  165 GLN cc_start: 0.8637 (tp40) cc_final: 0.8384 (tp40)
  outliers start: 16
  outliers final: 6
  residues processed: 105
  average time/residue: 0.5954
  time to fit residues: 66.5554
Evaluate side-chains
  96 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  442 MET
Chi-restraints excluded: chain B residue  517 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0980
   chunk 8 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 60 optimal weight:   30.0000
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.2188

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.138028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.085665 restraints weight = 16072.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 3.66
r_work: 0.2985 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   8852  Z= 0.231
  Angle     :  0.583   8.921  11982  Z= 0.300
  Chirality :  0.047   0.169   1361
  Planarity :  0.004   0.033   1556
  Dihedral  :  6.017  51.546   1264
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.09 %
    Favored  : 86.67 %
  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 are not related in a simple way.
  whole:  0.43 (0.26), residues: 1115
  helix:  1.15 (0.26), residues: 393
  sheet:  0.76 (0.33), residues: 238
  loop : -0.64 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.023   0.002   TYR A 473 
 PHE   0.018   0.001   PHE A 345 
 TRP   0.013   0.001   TRP A 233 
 HIS   0.007   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 8851)
  covalent geometry    : angle       0.58345 (11982)
  hydrogen bonds       : bond        0.04924 (  383)
  hydrogen bonds       : angle       4.67988 ( 1125)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  392 ASN cc_start: 0.8797 (t0) cc_final: 0.8429 (t0)
REVERT: A  693 MET cc_start: 0.2815 (OUTLIER) cc_final: 0.2288 (mpm)
REVERT: B  459 GLU cc_start: 0.6258 (tm-30) cc_final: 0.5850 (tm-30)
REVERT: B  518 ASP cc_start: 0.8730 (m-30) cc_final: 0.8261 (m-30)
REVERT: F   58 GLN cc_start: 0.7510 (tp40) cc_final: 0.7092 (tp40)
REVERT: F   61 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.7772 (mtm-85)
REVERT: F  165 GLN cc_start: 0.8713 (tp40) cc_final: 0.8501 (tp40)
  outliers start: 21
  outliers final: 10
  residues processed: 100
  average time/residue: 0.5564
  time to fit residues: 59.3016
Evaluate side-chains
  96 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  517 CYS
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   chunk 79 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 137 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.139534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.087590 restraints weight = 15992.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 3.59
r_work: 0.3028 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8852  Z= 0.126
  Angle     :  0.534   9.477  11982  Z= 0.270
  Chirality :  0.044   0.217   1361
  Planarity :  0.003   0.029   1556
  Dihedral  :  5.896  56.499   1264
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.79 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.26), residues: 1115
  helix:  1.32 (0.27), residues: 394
  sheet:  0.65 (0.33), residues: 233
  loop : -0.66 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.018   0.001   TYR B 417 
 PHE   0.010   0.001   PHE F 122 
 TRP   0.014   0.001   TRP A 233 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8851)
  covalent geometry    : angle       0.53382 (11982)
  hydrogen bonds       : bond        0.03872 (  383)
  hydrogen bonds       : angle       4.49464 ( 1125)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 PHE cc_start: 0.8627 (p90) cc_final: 0.8407 (p90)
REVERT: A  693 MET cc_start: 0.2752 (OUTLIER) cc_final: 0.2222 (mpm)
  outliers start: 17
  outliers final: 10
  residues processed: 102
  average time/residue: 0.5628
  time to fit residues: 61.2883
Evaluate side-chains
  93 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  124 MET
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  517 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 75 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 62 optimal weight:   40.0000
   chunk 15 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.137122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.084892 restraints weight = 16041.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 3.60
r_work: 0.2971 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8852  Z= 0.226
  Angle     :  0.594   9.742  11982  Z= 0.301
  Chirality :  0.046   0.153   1361
  Planarity :  0.004   0.032   1556
  Dihedral  :  5.974  55.349   1264
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.43 %
    Favored  : 84.22 %
  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 are not related in a simple way.
  whole:  0.35 (0.25), residues: 1115
  helix:  1.17 (0.27), residues: 392
  sheet:  0.71 (0.33), residues: 230
  loop : -0.73 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.019   0.001   TYR B 417 
 PHE   0.015   0.001   PHE F 122 
 TRP   0.019   0.001   TRP A 233 
 HIS   0.007   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 8851)
  covalent geometry    : angle       0.59381 (11982)
  hydrogen bonds       : bond        0.04820 (  383)
  hydrogen bonds       : angle       4.63032 ( 1125)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 PHE cc_start: 0.8803 (p90) cc_final: 0.8400 (p90)
REVERT: A  693 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.2505 (mpm)
REVERT: B  459 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5689 (tm-30)
REVERT: B  518 ASP cc_start: 0.8727 (m-30) cc_final: 0.8268 (m-30)
REVERT: F  243 GLU cc_start: 0.9031 (mp0) cc_final: 0.8817 (mp0)
  outliers start: 22
  outliers final: 13
  residues processed: 96
  average time/residue: 0.6079
  time to fit residues: 62.0757
Evaluate side-chains
  94 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  517 CYS
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 64 optimal weight:   50.0000
   chunk 13 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.136184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.084256 restraints weight = 16035.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 3.38
r_work: 0.2958 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   8852  Z= 0.263
  Angle     :  0.621  10.884  11982  Z= 0.316
  Chirality :  0.047   0.192   1361
  Planarity :  0.004   0.036   1556
  Dihedral  :  6.075  58.623   1264
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.93 %
    Favored  : 82.84 %
  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 are not related in a simple way.
  whole:  0.20 (0.25), residues: 1115
  helix:  1.01 (0.26), residues: 393
  sheet:  0.53 (0.32), residues: 237
  loop : -0.75 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 257 
 TYR   0.021   0.002   TYR B 417 
 PHE   0.025   0.002   PHE A 345 
 TRP   0.019   0.002   TRP A 233 
 HIS   0.006   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 8851)
  covalent geometry    : angle       0.62124 (11982)
  hydrogen bonds       : bond        0.05047 (  383)
  hydrogen bonds       : angle       4.67671 ( 1125)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  693 MET cc_start: 0.3399 (OUTLIER) cc_final: 0.2895 (mpm)
REVERT: B  459 GLU cc_start: 0.6354 (tm-30) cc_final: 0.5777 (tm-30)
REVERT: B  518 ASP cc_start: 0.8727 (m-30) cc_final: 0.8293 (m-30)
REVERT: F  243 GLU cc_start: 0.9036 (mp0) cc_final: 0.8797 (mp0)
  outliers start: 21
  outliers final: 14
  residues processed: 97
  average time/residue: 0.6720
  time to fit residues: 69.1678
Evaluate side-chains
  95 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  517 CYS
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 86 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.138878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.087356 restraints weight = 15884.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 3.40
r_work: 0.3016 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8852  Z= 0.122
  Angle     :  0.580  10.099  11982  Z= 0.289
  Chirality :  0.044   0.149   1361
  Planarity :  0.003   0.030   1556
  Dihedral  :  5.899  57.600   1264
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.25 %
    Favored  : 82.84 %
  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 are not related in a simple way.
  whole:  0.37 (0.26), residues: 1115
  helix:  1.29 (0.27), residues: 394
  sheet:  0.62 (0.33), residues: 228
  loop : -0.77 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.023   0.001   TYR B 417 
 PHE   0.013   0.001   PHE A 345 
 TRP   0.022   0.001   TRP A 233 
 HIS   0.003   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8851)
  covalent geometry    : angle       0.57971 (11982)
  hydrogen bonds       : bond        0.03823 (  383)
  hydrogen bonds       : angle       4.43461 ( 1125)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7996 (mmm160)
REVERT: A  271 GLU cc_start: 0.7677 (mp0) cc_final: 0.7400 (mp0)
REVERT: A  693 MET cc_start: 0.3152 (OUTLIER) cc_final: 0.2814 (mpm)
REVERT: B  459 GLU cc_start: 0.6112 (tm-30) cc_final: 0.5745 (tm-30)
REVERT: F  243 GLU cc_start: 0.9041 (mp0) cc_final: 0.8838 (mp0)
  outliers start: 18
  outliers final: 12
  residues processed: 98
  average time/residue: 0.5922
  time to fit residues: 61.9167
Evaluate side-chains
  93 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  666 MET
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 60 optimal weight:   30.0000
   chunk 78 optimal weight:    4.9990
   chunk 19 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 190 ASN
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  58 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.137950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.086951 restraints weight = 15968.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 3.16
r_work: 0.3015 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8852  Z= 0.141
  Angle     :  0.582  11.623  11982  Z= 0.291
  Chirality :  0.045   0.321   1361
  Planarity :  0.004   0.043   1556
  Dihedral  :  5.807  57.742   1264
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.78 %
    Favored  : 82.73 %
  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 are not related in a simple way.
  whole:  0.39 (0.26), residues: 1115
  helix:  1.34 (0.27), residues: 394
  sheet:  0.66 (0.33), residues: 228
  loop : -0.80 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.024   0.001   TYR B 417 
 PHE   0.016   0.001   PHE A 345 
 TRP   0.023   0.001   TRP A 233 
 HIS   0.004   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8851)
  covalent geometry    : angle       0.58219 (11982)
  hydrogen bonds       : bond        0.03998 (  383)
  hydrogen bonds       : angle       4.41010 ( 1125)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 GLU cc_start: 0.7641 (mp0) cc_final: 0.7335 (mp0)
REVERT: A  693 MET cc_start: 0.2942 (OUTLIER) cc_final: 0.2613 (mpm)
REVERT: B  459 GLU cc_start: 0.6139 (tm-30) cc_final: 0.5766 (tm-30)
REVERT: F  197 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.8219 (mtp)
  outliers start: 14
  outliers final: 13
  residues processed: 91
  average time/residue: 0.6095
  time to fit residues: 58.9999
Evaluate side-chains
  93 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  666 MET
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain F residue  197 MET
Chi-restraints excluded: chain F residue  239 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 17 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 60 optimal weight:   20.0000
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.138169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.087357 restraints weight = 16071.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 3.15
r_work: 0.3023 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8852  Z= 0.140
  Angle     :  0.597  12.247  11982  Z= 0.295
  Chirality :  0.045   0.303   1361
  Planarity :  0.004   0.044   1556
  Dihedral  :  5.767  58.322   1264
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 16.10 %
    Favored  : 82.62 %
  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 are not related in a simple way.
  whole:  0.43 (0.26), residues: 1115
  helix:  1.44 (0.27), residues: 388
  sheet:  0.67 (0.33), residues: 228
  loop : -0.82 (0.29), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 135 
 TYR   0.021   0.001   TYR B 417 
 PHE   0.018   0.001   PHE A 345 
 TRP   0.024   0.001   TRP A 233 
 HIS   0.003   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8851)
  covalent geometry    : angle       0.59674 (11982)
  hydrogen bonds       : bond        0.03900 (  383)
  hydrogen bonds       : angle       4.40336 ( 1125)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 GLU cc_start: 0.7673 (mp0) cc_final: 0.7364 (mp0)
REVERT: A  693 MET cc_start: 0.2922 (OUTLIER) cc_final: 0.2582 (mpm)
REVERT: B  459 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5794 (tm-30)
  outliers start: 12
  outliers final: 11
  residues processed: 93
  average time/residue: 0.5833
  time to fit residues: 57.4928
Evaluate side-chains
  93 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  666 MET
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  421 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 61 optimal weight:   40.0000
   chunk 89 optimal weight:   20.0000
   chunk 52 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 36 optimal weight:    0.2980
   chunk 13 optimal weight:    0.0670
   chunk 91 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.139198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.087949 restraints weight = 15899.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 3.35
r_work: 0.3026 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8852  Z= 0.112
  Angle     :  0.588  12.308  11982  Z= 0.288
  Chirality :  0.045   0.305   1361
  Planarity :  0.004   0.050   1556
  Dihedral  :  5.688  59.858   1264
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.41 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.10 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.26), residues: 1115
  helix:  1.54 (0.27), residues: 389
  sheet:  0.66 (0.34), residues: 227
  loop : -0.79 (0.29), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 135 
 TYR   0.020   0.001   TYR B 417 
 PHE   0.010   0.001   PHE A 345 
 TRP   0.021   0.001   TRP A 233 
 HIS   0.003   0.000   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8851)
  covalent geometry    : angle       0.58834 (11982)
  hydrogen bonds       : bond        0.03521 (  383)
  hydrogen bonds       : angle       4.33826 ( 1125)
  Misc. bond           : bond        0.00001 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3192.57 seconds
wall clock time: 55 minutes 4.07 seconds (3304.07 seconds total)