Starting phenix.real_space_refine
on Sat May  2 22:07:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zux_60500/05_2026/8zux_60500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zux_60500/05_2026/8zux_60500.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zux_60500/05_2026/8zux_60500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zux_60500/05_2026/8zux_60500.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zux_60500/05_2026/8zux_60500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zux_60500/05_2026/8zux_60500.map"
  }
  resolution = 2.68
  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       6      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    5420      2.51       5
     N    1514      2.21       5
     O    1639      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8626
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4659
          Classifications: {'peptide': 598}
          Link IDs: {'PTRANS': 21, 'TRANS': 576}
    Chain: "B"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 1906
          Classifications: {'peptide': 247}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 231}
    Chain: "F"
      Number of atoms: 1973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1973
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 36
          Unusual residues: {' MG': 1, 'ATP': 1, 'BCT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "F"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'1VU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.25
  Number of scatterers: 8626
  At special positions: 0
  Unit cell: (98.28, 98.28, 134.4, 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      46     16.00
     P       6     15.00
     Mg      1     11.99
     O    1639      8.00
     N    1514      7.00
     C    5420      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 318.3 milliseconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 13 sheets defined
      42.5% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 86
      removed outlier: 3.863A  pdb=" N   ALA A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 4.471A  pdb=" N   SER A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 106
      removed outlier: 3.514A  pdb=" N   LYS A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 135
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.766A  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 176 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 358 through 366
    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 647
    Processing helix  chain 'A' and resid 648 through 650
      No H-bonds generated for 'chain 'A' and resid 648 through 650'
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.938A  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: 3.512A  pdb=" N   LYS B 414 " --> pdb=" O   ARG B 410 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU B 415 " --> pdb=" O   HIS B 411 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B 416 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 442
      removed outlier: 3.831A  pdb=" N   ASP B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
    Processing helix  chain 'B' and resid 464 through 473
    Processing helix  chain 'B' and resid 479 through 491
      removed outlier: 3.652A  pdb=" N   GLN B 483 " --> pdb=" O   VAL B 479 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   ALA B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 499
      removed outlier: 3.750A  pdb=" N   ARG B 499 " --> pdb=" O   PRO B 495 " (cutoff:3.500A)
    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 522
      removed outlier: 3.511A  pdb=" N   ASP B 518 " --> pdb=" O   ARG B 514 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 33 through 48
    Processing helix  chain 'F' and resid 51 through 61
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 97 through 101
    Processing helix  chain 'F' and resid 128 through 132
    Processing helix  chain 'F' and resid 134 through 152
    Processing helix  chain 'F' and resid 169 through 187
      removed outlier: 3.698A  pdb=" N   LEU F 173 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 211
      removed outlier: 3.659A  pdb=" N   ALA F 209 " --> pdb=" O   VAL F 205 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 227 through 235
    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
      removed outlier: 3.615A  pdb=" N   ASN F 276 " --> pdb=" O   ARG F 272 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 3.772A  pdb=" N   ILE A  92 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   HIS A 140 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU A  67 " --> pdb=" O   HIS A 140 " (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 283
    Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 283
      removed outlier: 6.327A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR A 346 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294
    Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416
    Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 421
    Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 565
      removed outlier: 6.445A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.511A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.698A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.511A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.698A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LYS B 426 " --> pdb=" O   THR B 451 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   TYR B 453 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   THR B 428 " --> pdb=" O   TYR B 453 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 80 through 82
      removed outlier: 4.530A  pdb=" N   THR F 109 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG F 259 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 199 through 201

    431 hydrogen bonds defined for protein.
    1197 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: 1.53

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1458
        1.28 -     1.42: 2162
        1.42 -     1.56: 5077
        1.56 -     1.70: 17
        1.70 -     1.84: 74
  Bond restraints: 8788
  Sorted by residual:
  bond pdb=" O10 1VU F5601 "
       pdb=" P1  1VU F5601 "
    ideal  model  delta    sigma   weight residual
    2.250  1.642  0.608 2.00e-02 2.50e+03 9.24e+02
  bond pdb=" O14 1VU F5601 "
       pdb=" P2  1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.682  1.468  0.214 2.00e-02 2.50e+03 1.15e+02
  bond pdb=" C16 1VU F5601 "
       pdb=" C22 1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.560  1.360  0.200 2.00e-02 2.50e+03 9.99e+01
  bond pdb=" C16 1VU F5601 "
       pdb=" O11 1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.425  1.590 -0.165 2.00e-02 2.50e+03 6.83e+01
  bond pdb=" C15 1VU F5601 "
       pdb=" O11 1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.459  1.304  0.155 2.00e-02 2.50e+03 5.99e+01
  ... (remaining 8783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.19: 11888
       11.19 -    22.38: 6
       22.38 -    33.57: 3
       33.57 -    44.76: 0
       44.76 -    55.95: 1
  Bond angle restraints: 11898
  Sorted by residual:
  angle pdb=" O14 1VU F5601 "
        pdb=" P2  1VU F5601 "
        pdb=" O15 1VU F5601 "
      ideal   model   delta    sigma   weight residual
      53.72  109.67  -55.95 3.00e+00 1.11e-01 3.48e+02
  angle pdb=" O8  1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O9  1VU F5601 "
      ideal   model   delta    sigma   weight residual
     140.21  108.86   31.35 3.00e+00 1.11e-01 1.09e+02
  angle pdb=" O10 1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O9  1VU F5601 "
      ideal   model   delta    sigma   weight residual
      78.74  109.41  -30.67 3.00e+00 1.11e-01 1.05e+02
  angle pdb=" O10 1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O7  1VU F5601 "
      ideal   model   delta    sigma   weight residual
      85.76  109.95  -24.19 3.00e+00 1.11e-01 6.50e+01
  angle pdb=" P   1VU F5601 "
        pdb=" O7  1VU F5601 "
        pdb=" P1  1VU F5601 "
      ideal   model   delta    sigma   weight residual
     143.93  123.76   20.17 3.00e+00 1.11e-01 4.52e+01
  ... (remaining 11893 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.34: 5224
       31.34 -    62.67: 123
       62.67 -    94.01: 12
       94.01 -   125.35: 2
      125.35 -   156.69: 5
  Dihedral angle restraints: 5366
    sinusoidal: 2192
      harmonic: 3174
  Sorted by residual:
  dihedral pdb=" C15 1VU F5601 "
           pdb=" C23 1VU F5601 "
           pdb=" O13 1VU F5601 "
           pdb=" P2  1VU F5601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      86.09  -70.60  156.69     1      3.00e+01 1.11e-03 2.05e+01
  dihedral pdb=" C22 1VU F5601 "
           pdb=" C23 1VU F5601 "
           pdb=" O13 1VU F5601 "
           pdb=" P2  1VU F5601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     328.48  173.32  155.16     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" C   1VU F5601 "
           pdb=" C1  1VU F5601 "
           pdb=" C2  1VU F5601 "
           pdb=" O   1VU F5601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -123.88   22.57 -146.45     1      3.00e+01 1.11e-03 1.96e+01
  ... (remaining 5363 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 1316
       0.121 -    0.243: 15
       0.243 -    0.364: 1
       0.364 -    0.486: 0
       0.486 -    0.607: 1
  Chirality restraints: 1333
  Sorted by residual:
  chirality pdb=" C22 1VU F5601 "
            pdb=" C16 1VU F5601 "
            pdb=" C23 1VU F5601 "
            pdb=" O12 1VU F5601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.99   -2.38   -0.61 2.00e-01 2.50e+01 9.23e+00
  chirality pdb=" C9  1VU F5601 "
            pdb=" C10 1VU F5601 "
            pdb=" C8  1VU F5601 "
            pdb=" O3  1VU F5601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.68    2.40    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" C16 1VU F5601 "
            pdb=" C22 1VU F5601 "
            pdb=" N2  1VU F5601 "
            pdb=" O11 1VU F5601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.48    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1330 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   BCT A 803 "   -0.063 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" O1  BCT A 803 "    0.024 2.00e-02 2.50e+03
        pdb=" O2  BCT A 803 "    0.024 2.00e-02 2.50e+03
        pdb=" O3  BCT A 803 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 394 "   -0.019 2.00e-02 2.50e+03   2.04e-02 1.04e+01
        pdb=" CG  TRP A 394 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 394 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 394 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 394 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 394 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 394 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 394 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 394 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 394 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F 178 "   -0.007 2.00e-02 2.50e+03   1.49e-02 2.21e+00
        pdb=" C   ASP F 178 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ASP F 178 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE F 179 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 130
        2.67 -     3.23: 8102
        3.23 -     3.79: 13104
        3.79 -     4.34: 18292
        4.34 -     4.90: 30574
  Nonbonded interactions: 70202
  Sorted by model distance:
  nonbonded pdb=" O2G ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.116 2.170
  nonbonded pdb=" OE1 GLU A 349 "
            pdb="MG    MG A 802 "
     model   vdw
     2.124 2.170
  nonbonded pdb=" OD2 ASP F 105 "
            pdb=" OG  SER F 134 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   THR A 361 "
            pdb=" OG1 THR A 365 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O1A ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.226 2.170
  ... (remaining 70197 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:                  0.000
  Normalize map: mean=0, sd=1:             5.320
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.120
  Find NCS groups from input model:        0.050
  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:7.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.608   8788  Z= 0.457
  Angle     :  0.983  55.946  11898  Z= 0.398
  Chirality :  0.047   0.607   1333
  Planarity :  0.004   0.037   1544
  Dihedral  : 14.628 156.687   3324
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  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:  0.27 (0.26), residues: 1100
  helix:  0.93 (0.26), residues: 433
  sheet:  0.58 (0.34), residues: 237
  loop : -0.75 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 210 
 TYR   0.023   0.001   TYR A 473 
 PHE   0.010   0.001   PHE F 122 
 TRP   0.052   0.003   TRP A 394 
 HIS   0.003   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00920 ( 8788)
  covalent geometry    : angle       0.98283 (11898)
  hydrogen bonds       : bond        0.14039 (  413)
  hydrogen bonds       : angle       5.81702 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  155 CYS cc_start: 0.8239 (m) cc_final: 0.6565 (m)
REVERT: A  230 ARG cc_start: 0.8889 (ptp90) cc_final: 0.8147 (ptp90)
REVERT: F  241 GLN cc_start: 0.8803 (mt0) cc_final: 0.8582 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.8583
  time to fit residues: 102.2091
Evaluate side-chains
  89 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0050
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
F 236 ASN
F 283 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.106837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.066523 restraints weight = 13670.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 2.14
r_work: 0.2603 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2481 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9070
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8788  Z= 0.140
  Angle     :  0.565   7.427  11898  Z= 0.294
  Chirality :  0.045   0.229   1333
  Planarity :  0.004   0.038   1544
  Dihedral  : 12.928 133.745   1297
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.10 %
    Favored  : 92.92 %
  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 (0.25), residues: 1100
  helix:  1.30 (0.26), residues: 435
  sheet:  0.59 (0.34), residues: 234
  loop : -0.63 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 207 
 TYR   0.013   0.001   TYR B 486 
 PHE   0.020   0.001   PHE A 263 
 TRP   0.016   0.002   TRP A 394 
 HIS   0.004   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8788)
  covalent geometry    : angle       0.56511 (11898)
  hydrogen bonds       : bond        0.04303 (  413)
  hydrogen bonds       : angle       4.48856 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.8670 (pm20) cc_final: 0.8284 (tm-30)
REVERT: A  230 ARG cc_start: 0.9106 (ptp90) cc_final: 0.8218 (ptt-90)
REVERT: A  244 LEU cc_start: 0.9644 (mt) cc_final: 0.9284 (tm)
REVERT: B  499 ARG cc_start: 0.9027 (mpp-170) cc_final: 0.8799 (mtm-85)
REVERT: F  147 GLN cc_start: 0.9146 (tt0) cc_final: 0.8836 (tt0)
REVERT: F  171 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8340 (mm-30)
REVERT: F  241 GLN cc_start: 0.9104 (mt0) cc_final: 0.8868 (tt0)
  outliers start: 9
  outliers final: 1
  residues processed: 98
  average time/residue: 0.7880
  time to fit residues: 81.1305
Evaluate side-chains
  91 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 355 GLN
F 236 ASN
F 283 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.106162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.065813 restraints weight = 13641.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 2.10
r_work: 0.2587 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2464 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9111
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8788  Z= 0.148
  Angle     :  0.548   8.509  11898  Z= 0.284
  Chirality :  0.045   0.221   1333
  Planarity :  0.004   0.037   1544
  Dihedral  : 11.511 118.515   1297
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.17 %
    Favored  : 91.07 %
  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:  0.68 (0.26), residues: 1100
  helix:  1.48 (0.26), residues: 435
  sheet:  0.54 (0.34), residues: 234
  loop : -0.62 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 154 
 TYR   0.019   0.001   TYR B 486 
 PHE   0.033   0.002   PHE A 307 
 TRP   0.015   0.002   TRP A 233 
 HIS   0.004   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8788)
  covalent geometry    : angle       0.54807 (11898)
  hydrogen bonds       : bond        0.04033 (  413)
  hydrogen bonds       : angle       4.27460 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8492 (tmm-80)
REVERT: A  155 CYS cc_start: 0.8590 (m) cc_final: 0.7424 (m)
REVERT: A  188 GLU cc_start: 0.8683 (pm20) cc_final: 0.8323 (tm-30)
REVERT: A  230 ARG cc_start: 0.9214 (ptp90) cc_final: 0.8561 (ptt-90)
REVERT: A  265 ASP cc_start: 0.8911 (t0) cc_final: 0.8475 (p0)
REVERT: A  448 MET cc_start: 0.9336 (ttm) cc_final: 0.9127 (ttp)
REVERT: B  488 GLU cc_start: 0.9233 (tt0) cc_final: 0.8750 (tm-30)
REVERT: B  499 ARG cc_start: 0.9033 (mpp-170) cc_final: 0.8790 (mtm180)
REVERT: F  147 GLN cc_start: 0.9160 (tt0) cc_final: 0.8860 (tt0)
REVERT: F  171 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8448 (mm-30)
  outliers start: 7
  outliers final: 2
  residues processed: 94
  average time/residue: 0.8407
  time to fit residues: 82.8712
Evaluate side-chains
  88 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  327 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0770
   chunk 56 optimal weight:    0.8980
   chunk 21 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
F 236 ASN
F 270 ASN
F 283 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.106991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.066697 restraints weight = 13820.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 2.14
r_work: 0.2606 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2485 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9074
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8788  Z= 0.118
  Angle     :  0.528   8.615  11898  Z= 0.272
  Chirality :  0.044   0.229   1333
  Planarity :  0.004   0.040   1544
  Dihedral  : 10.863 110.561   1297
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.71 %
    Favored  : 90.20 %
  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 are not related in a simple way.
  whole:  0.74 (0.26), residues: 1100
  helix:  1.52 (0.26), residues: 436
  sheet:  0.64 (0.34), residues: 229
  loop : -0.60 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 207 
 TYR   0.010   0.001   TYR F 206 
 PHE   0.022   0.001   PHE A 307 
 TRP   0.012   0.001   TRP A 233 
 HIS   0.003   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8788)
  covalent geometry    : angle       0.52764 (11898)
  hydrogen bonds       : bond        0.03591 (  413)
  hydrogen bonds       : angle       4.17447 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8701 (ttm) cc_final: 0.8318 (mtt)
REVERT: A  155 CYS cc_start: 0.8666 (m) cc_final: 0.8150 (m)
REVERT: A  172 GLN cc_start: 0.8883 (pp30) cc_final: 0.8683 (pp30)
REVERT: A  188 GLU cc_start: 0.8682 (pm20) cc_final: 0.8335 (tm-30)
REVERT: A  230 ARG cc_start: 0.9231 (ptp90) cc_final: 0.8537 (ptt-90)
REVERT: A  265 ASP cc_start: 0.8895 (t0) cc_final: 0.8453 (p0)
REVERT: A  448 MET cc_start: 0.9326 (ttm) cc_final: 0.9125 (ttp)
REVERT: B  488 GLU cc_start: 0.9217 (tt0) cc_final: 0.8767 (tm-30)
REVERT: B  499 ARG cc_start: 0.9019 (mpp-170) cc_final: 0.8537 (mtm180)
REVERT: F  147 GLN cc_start: 0.9136 (tt0) cc_final: 0.8811 (tt0)
REVERT: F  171 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8308 (mp0)
  outliers start: 10
  outliers final: 5
  residues processed: 99
  average time/residue: 0.7631
  time to fit residues: 79.4727
Evaluate side-chains
  92 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain F residue  253 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
F 283 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.105923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.065637 restraints weight = 13805.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 2.12
r_work: 0.2586 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2464 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9089
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8788  Z= 0.142
  Angle     :  0.541   8.542  11898  Z= 0.280
  Chirality :  0.045   0.234   1333
  Planarity :  0.004   0.047   1544
  Dihedral  : 10.334 102.156   1297
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  8.82 %
    Favored  : 89.65 %
  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 are not related in a simple way.
  whole:  0.77 (0.25), residues: 1100
  helix:  1.52 (0.26), residues: 436
  sheet:  0.64 (0.34), residues: 228
  loop : -0.55 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 207 
 TYR   0.011   0.001   TYR F 206 
 PHE   0.018   0.001   PHE A 307 
 TRP   0.013   0.001   TRP A 233 
 HIS   0.004   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8788)
  covalent geometry    : angle       0.54143 (11898)
  hydrogen bonds       : bond        0.03825 (  413)
  hydrogen bonds       : angle       4.16119 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8395 (mtt)
REVERT: A  155 CYS cc_start: 0.8771 (m) cc_final: 0.8275 (m)
REVERT: A  172 GLN cc_start: 0.8908 (pp30) cc_final: 0.8681 (pp30)
REVERT: A  188 GLU cc_start: 0.8707 (pm20) cc_final: 0.8373 (tm-30)
REVERT: A  230 ARG cc_start: 0.9298 (ptp90) cc_final: 0.8592 (ptt-90)
REVERT: A  265 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8440 (p0)
REVERT: B  488 GLU cc_start: 0.9243 (tt0) cc_final: 0.8846 (tm-30)
REVERT: B  499 ARG cc_start: 0.9025 (mpp-170) cc_final: 0.8797 (mtm-85)
REVERT: F  147 GLN cc_start: 0.9133 (tt0) cc_final: 0.8805 (tt0)
REVERT: F  171 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8412 (mp0)
  outliers start: 14
  outliers final: 6
  residues processed: 101
  average time/residue: 0.8096
  time to fit residues: 85.6571
Evaluate side-chains
  95 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue  299 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 73 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
F 236 ASN
F 283 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.105141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.064554 restraints weight = 13712.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 2.12
r_work: 0.2565 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2443 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9129
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8788  Z= 0.190
  Angle     :  0.570   8.407  11898  Z= 0.295
  Chirality :  0.046   0.239   1333
  Planarity :  0.004   0.051   1544
  Dihedral  :  9.939 102.568   1297
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.91 %
    Favored  : 88.56 %
  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:  0.75 (0.26), residues: 1100
  helix:  1.49 (0.26), residues: 436
  sheet:  0.67 (0.34), residues: 231
  loop : -0.57 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 207 
 TYR   0.012   0.001   TYR F 206 
 PHE   0.017   0.001   PHE F 122 
 TRP   0.014   0.002   TRP A 233 
 HIS   0.005   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8788)
  covalent geometry    : angle       0.56972 (11898)
  hydrogen bonds       : bond        0.04225 (  413)
  hydrogen bonds       : angle       4.22485 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 CYS cc_start: 0.8816 (m) cc_final: 0.8377 (m)
REVERT: A  188 GLU cc_start: 0.8670 (pm20) cc_final: 0.8360 (tm-30)
REVERT: A  265 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8448 (p0)
REVERT: B  488 GLU cc_start: 0.9250 (tt0) cc_final: 0.8869 (tm-30)
REVERT: B  499 ARG cc_start: 0.9050 (mpp-170) cc_final: 0.8800 (mtm-85)
REVERT: F  147 GLN cc_start: 0.9153 (tt0) cc_final: 0.8843 (tt0)
REVERT: F  171 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8440 (mp0)
REVERT: F  266 ASP cc_start: 0.9088 (t70) cc_final: 0.8796 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 98
  average time/residue: 0.8545
  time to fit residues: 87.6961
Evaluate side-chains
  93 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain F residue  253 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0050
   chunk 90 optimal weight:    0.9980
   chunk 105 optimal weight:    0.3980
   chunk 70 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
F 283 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.105081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.064723 restraints weight = 13959.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.2690 rms_B_bonded: 2.13
r_work: 0.2565 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2444 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9105
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8788  Z= 0.176
  Angle     :  0.578  10.230  11898  Z= 0.298
  Chirality :  0.046   0.241   1333
  Planarity :  0.004   0.056   1544
  Dihedral  :  9.670 102.037   1297
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.11 %
    Favored  : 87.58 %
  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:  0.78 (0.26), residues: 1100
  helix:  1.54 (0.26), residues: 436
  sheet:  0.65 (0.34), residues: 233
  loop : -0.57 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 243 
 TYR   0.013   0.001   TYR F 206 
 PHE   0.015   0.001   PHE F 122 
 TRP   0.014   0.002   TRP A 233 
 HIS   0.005   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 8788)
  covalent geometry    : angle       0.57762 (11898)
  hydrogen bonds       : bond        0.04103 (  413)
  hydrogen bonds       : angle       4.22256 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8812 (ttm) cc_final: 0.8510 (mtt)
REVERT: A  155 CYS cc_start: 0.8851 (m) cc_final: 0.8367 (m)
REVERT: A  188 GLU cc_start: 0.8681 (pm20) cc_final: 0.8335 (tm-30)
REVERT: A  265 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8498 (p0)
REVERT: B  488 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8870 (tm-30)
REVERT: B  499 ARG cc_start: 0.9031 (mpp-170) cc_final: 0.8746 (mtm-85)
REVERT: F   53 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8346 (ttp80)
REVERT: F  147 GLN cc_start: 0.9142 (tt0) cc_final: 0.8813 (tt0)
REVERT: F  171 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8407 (mp0)
REVERT: F  266 ASP cc_start: 0.9086 (t70) cc_final: 0.8819 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 95
  average time/residue: 0.8359
  time to fit residues: 83.2717
Evaluate side-chains
  93 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  488 GLU
Chi-restraints excluded: chain F residue  253 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 108 optimal weight:    0.4980
   chunk 73 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
F 236 ASN
F 283 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.106228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.066095 restraints weight = 13720.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2721 rms_B_bonded: 2.12
r_work: 0.2598 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2476 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9105
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8788  Z= 0.123
  Angle     :  0.573  17.231  11898  Z= 0.289
  Chirality :  0.045   0.245   1333
  Planarity :  0.004   0.059   1544
  Dihedral  :  9.312 104.013   1297
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.33 %
    Favored  : 87.36 %
  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:  0.82 (0.26), residues: 1100
  helix:  1.54 (0.26), residues: 437
  sheet:  0.62 (0.34), residues: 233
  loop : -0.48 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 243 
 TYR   0.011   0.001   TYR F 206 
 PHE   0.014   0.001   PHE A 307 
 TRP   0.012   0.001   TRP A 233 
 HIS   0.004   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8788)
  covalent geometry    : angle       0.57294 (11898)
  hydrogen bonds       : bond        0.03576 (  413)
  hydrogen bonds       : angle       4.17647 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8823 (ttm) cc_final: 0.8538 (mtt)
REVERT: A  155 CYS cc_start: 0.8860 (m) cc_final: 0.8383 (m)
REVERT: A  188 GLU cc_start: 0.8677 (pm20) cc_final: 0.8357 (tm-30)
REVERT: A  230 ARG cc_start: 0.9275 (ptp90) cc_final: 0.8643 (ptp90)
REVERT: A  265 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8517 (p0)
REVERT: B  488 GLU cc_start: 0.9234 (tt0) cc_final: 0.8875 (tm-30)
REVERT: B  499 ARG cc_start: 0.9054 (mpp-170) cc_final: 0.8766 (mtm-85)
REVERT: F  147 GLN cc_start: 0.9145 (tt0) cc_final: 0.8834 (tt0)
REVERT: F  171 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8418 (mp0)
REVERT: F  266 ASP cc_start: 0.9017 (t70) cc_final: 0.8713 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 96
  average time/residue: 0.8059
  time to fit residues: 81.0940
Evaluate side-chains
  94 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain F residue  253 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
F 283 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.106207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.066064 restraints weight = 13720.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 2.12
r_work: 0.2595 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2473 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9084
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8788  Z= 0.130
  Angle     :  0.587  19.117  11898  Z= 0.294
  Chirality :  0.045   0.247   1333
  Planarity :  0.004   0.063   1544
  Dihedral  :  9.191 102.751   1297
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 11.66 %
    Favored  : 87.25 %
  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:  0.86 (0.26), residues: 1100
  helix:  1.55 (0.26), residues: 437
  sheet:  0.63 (0.34), residues: 230
  loop : -0.42 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 243 
 TYR   0.011   0.001   TYR F 206 
 PHE   0.014   0.001   PHE A 307 
 TRP   0.011   0.001   TRP A 233 
 HIS   0.004   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8788)
  covalent geometry    : angle       0.58706 (11898)
  hydrogen bonds       : bond        0.03593 (  413)
  hydrogen bonds       : angle       4.16090 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8823 (ttm) cc_final: 0.8541 (mtt)
REVERT: A  155 CYS cc_start: 0.8864 (m) cc_final: 0.8383 (m)
REVERT: A  188 GLU cc_start: 0.8698 (pm20) cc_final: 0.8363 (tm-30)
REVERT: A  230 ARG cc_start: 0.9250 (ptp90) cc_final: 0.8593 (ptp90)
REVERT: A  265 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8487 (p0)
REVERT: B  488 GLU cc_start: 0.9246 (tt0) cc_final: 0.8862 (tm-30)
REVERT: B  499 ARG cc_start: 0.9036 (mpp-170) cc_final: 0.8730 (mtm-85)
REVERT: F   53 ARG cc_start: 0.8717 (mtm110) cc_final: 0.8321 (ttp80)
REVERT: F  147 GLN cc_start: 0.9126 (tt0) cc_final: 0.8798 (tt0)
REVERT: F  171 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8388 (mp0)
REVERT: F  266 ASP cc_start: 0.9024 (t70) cc_final: 0.8684 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 93
  average time/residue: 0.8412
  time to fit residues: 82.0762
Evaluate side-chains
  95 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain F residue  253 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0010
   chunk 19 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.9390

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

Flipped N/Q/H residues before XYZ refinement:
F 236 ASN
F 283 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.106177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.066016 restraints weight = 13703.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.12
r_work: 0.2583 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2462 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9086
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8788  Z= 0.136
  Angle     :  0.603  21.090  11898  Z= 0.300
  Chirality :  0.045   0.248   1333
  Planarity :  0.004   0.066   1544
  Dihedral  :  9.128 102.276   1297
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.66 %
    Favored  : 87.15 %
  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:  0.86 (0.26), residues: 1100
  helix:  1.56 (0.26), residues: 437
  sheet:  0.63 (0.34), residues: 230
  loop : -0.41 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG A 243 
 TYR   0.011   0.001   TYR F 206 
 PHE   0.014   0.001   PHE A 307 
 TRP   0.010   0.001   TRP A 233 
 HIS   0.004   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8788)
  covalent geometry    : angle       0.60280 (11898)
  hydrogen bonds       : bond        0.03634 (  413)
  hydrogen bonds       : angle       4.15665 ( 1197)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 CYS cc_start: 0.8868 (m) cc_final: 0.8397 (m)
REVERT: A  188 GLU cc_start: 0.8690 (pm20) cc_final: 0.8366 (tm-30)
REVERT: A  230 ARG cc_start: 0.9221 (ptp90) cc_final: 0.8548 (ptp90)
REVERT: A  265 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8575 (p0)
REVERT: B  488 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8864 (tm-30)
REVERT: B  499 ARG cc_start: 0.9038 (mpp-170) cc_final: 0.8727 (mtm-85)
REVERT: F   53 ARG cc_start: 0.8715 (mtm110) cc_final: 0.8320 (ttp80)
REVERT: F  147 GLN cc_start: 0.9122 (tt0) cc_final: 0.8794 (tt0)
REVERT: F  171 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8388 (mp0)
REVERT: F  266 ASP cc_start: 0.9028 (t70) cc_final: 0.8745 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 94
  average time/residue: 0.8351
  time to fit residues: 82.3166
Evaluate side-chains
  98 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  488 GLU
Chi-restraints excluded: chain F residue  253 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
F 283 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.106523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.066430 restraints weight = 13695.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 2.11
r_work: 0.2602 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2480 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9077
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8788  Z= 0.124
  Angle     :  0.597  22.460  11898  Z= 0.295
  Chirality :  0.045   0.249   1333
  Planarity :  0.004   0.065   1544
  Dihedral  :  9.039 102.346   1297
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 11.87 %
    Favored  : 87.04 %
  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 are not related in a simple way.
  whole:  0.90 (0.26), residues: 1100
  helix:  1.60 (0.26), residues: 437
  sheet:  0.80 (0.34), residues: 222
  loop : -0.48 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 243 
 TYR   0.011   0.001   TYR F 206 
 PHE   0.014   0.001   PHE A 307 
 TRP   0.009   0.001   TRP A 233 
 HIS   0.003   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8788)
  covalent geometry    : angle       0.59712 (11898)
  hydrogen bonds       : bond        0.03478 (  413)
  hydrogen bonds       : angle       4.13039 ( 1197)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3855.22 seconds
wall clock time: 66 minutes 18.14 seconds (3978.14 seconds total)