Starting phenix.real_space_refine
on Sun May  3 00:24:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uhy_64180/05_2026/9uhy_64180.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uhy_64180/05_2026/9uhy_64180.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uhy_64180/05_2026/9uhy_64180.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uhy_64180/05_2026/9uhy_64180.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uhy_64180/05_2026/9uhy_64180.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uhy_64180/05_2026/9uhy_64180.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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      53      5.16       5
     C    5754      2.51       5
     N    1604      2.21       5
     O    1754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 9172
  Number of models: 1
  Model: ""
    Number of chains: 5
    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: 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: 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
    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: 2.08, per 1000 atoms: 0.23
  Number of scatterers: 9172
  At special positions: 0
  Unit cell: (95.76, 99.12, 136.08, 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      53     16.00
     P       6     15.00
     Mg      1     11.99
     O    1754      8.00
     N    1604      7.00
     C    5754      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: 1.00
  Conformation dependent library (CDL) restraints added in 356.8 milliseconds
  

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2176

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 10 sheets defined
      40.7% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 84
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.517A  pdb=" N   ALA A  98 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   SER A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 95 through 99'
    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
    Processing helix  chain 'A' and resid 149 through 160
      removed outlier: 3.556A  pdb=" N   ALA A 153 " --> pdb=" O   ASN A 149 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLU A 159 " --> pdb=" O   CYS A 155 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASP A 160 " --> pdb=" O   LEU A 156 " (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 212
      removed outlier: 3.590A  pdb=" N   ARG A 210 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLU A 211 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 253
      removed outlier: 4.242A  pdb=" N   ALA A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   SER A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 4.353A  pdb=" N   THR A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLU A 362 " --> pdb=" O   HIS A 358 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   CYS A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ILE A 364 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 357 through 364'
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'A' and resid 385 through 389
    Processing helix  chain 'A' and resid 458 through 472
    Processing helix  chain 'A' and resid 481 through 491
    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
      removed outlier: 3.749A  pdb=" N   LYS A 648 " --> pdb=" O   ALA A 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.885A  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
      removed outlier: 3.551A  pdb=" N   PHE B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 407
      removed outlier: 3.588A  pdb=" N   GLU B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 422
      removed outlier: 3.629A  pdb=" N   HIS B 411 " --> pdb=" O   GLY B 407 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 442
      removed outlier: 3.637A  pdb=" N   ASP B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
      removed outlier: 3.642A  pdb=" N   CYS B 448 " --> pdb=" O   LYS B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 473
    Processing helix  chain 'B' and resid 478 through 490
    Processing helix  chain 'B' and resid 493 through 499
      removed outlier: 3.650A  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
    Processing helix  chain 'B' and resid 523 through 525
      No H-bonds generated for 'chain 'B' and resid 523 through 525'
    Processing helix  chain 'F' and resid 34 through 49
      removed outlier: 4.020A  pdb=" N   ILE F  39 " --> pdb=" O   VAL F  35 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU F  40 " --> pdb=" O   ASN F  36 " (cutoff:3.500A)
    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: 4.103A  pdb=" N   LEU F 173 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 211
      removed outlier: 3.596A  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
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 3.608A  pdb=" N   ILE A  66 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE A  92 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 232
    Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351
      removed outlier: 4.140A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   HIS A 269 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   GLU A 289 " --> pdb=" O   HIS A 269 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   GLU A 271 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   GLU A 287 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLN A 273 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   SER A 291 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL A 300 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   GLN A 293 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LYS A 298 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 14.539A  pdb=" N   GLN A 297 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 10.903A  pdb=" N   TYR A 401 " --> pdb=" O   GLN A 297 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL A 299 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   TRP A 394 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   TYR A 455 " --> pdb=" O   TRP A 394 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL A 396 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   ILE A 453 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   CYS A 398 " --> pdb=" O   LYS A 451 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LYS A 451 " --> pdb=" O   CYS A 398 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL A 400 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 416
      removed outlier: 3.572A  pdb=" N   GLY A 415 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 421
    Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 565
      removed outlier: 6.563A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.523A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   ASP B 393 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLU B 459 " --> pdb=" O   ILE B 430 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ARG B 432 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   ALA B 461 " --> pdb=" O   ARG B 432 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ALA B 434 " --> pdb=" O   ALA B 461 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.523A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   ASP B 393 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   THR B 451 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 80 through 82
      removed outlier: 4.662A  pdb=" N   THR F 109 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG F 259 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 199 through 201

    427 hydrogen bonds defined for protein.
    1191 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: 1.58

  Time building geometry restraints manager: 1.25 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: 1560
        1.28 -     1.42: 2258
        1.42 -     1.56: 5416
        1.56 -     1.70: 19
        1.70 -     1.84: 86
  Bond restraints: 9339
  Sorted by residual:
  bond pdb=" O10 1VU F5601 "
       pdb=" P1  1VU F5601 "
    ideal  model  delta    sigma   weight residual
    2.250  1.643  0.607 2.00e-02 2.50e+03 9.22e+02
  bond pdb=" C2  BTN A 801 "
       pdb=" S1  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.824  1.437  0.387 2.00e-02 2.50e+03 3.75e+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  1.358  0.202 2.00e-02 2.50e+03 1.02e+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 9.40e+01
  ... (remaining 9334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.20: 12634
       11.20 -    22.41: 7
       22.41 -    33.61: 3
       33.61 -    44.81: 0
       44.81 -    56.01: 1
  Bond angle restraints: 12645
  Sorted by residual:
  angle pdb=" O14 1VU F5601 "
        pdb=" P2  1VU F5601 "
        pdb=" O15 1VU F5601 "
      ideal   model   delta    sigma   weight residual
      53.72  109.73  -56.01 3.00e+00 1.11e-01 3.49e+02
  angle pdb=" O8  1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O9  1VU F5601 "
      ideal   model   delta    sigma   weight residual
     140.21  109.22   30.99 3.00e+00 1.11e-01 1.07e+02
  angle pdb=" O10 1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O9  1VU F5601 "
      ideal   model   delta    sigma   weight residual
      78.74  109.51  -30.77 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  110.07  -24.31 3.00e+00 1.11e-01 6.57e+01
  angle pdb=" P   1VU F5601 "
        pdb=" O7  1VU F5601 "
        pdb=" P1  1VU F5601 "
      ideal   model   delta    sigma   weight residual
     143.93  122.94   20.99 3.00e+00 1.11e-01 4.90e+01
  ... (remaining 12640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.59: 5584
       34.59 -    69.18: 113
       69.18 -   103.77: 15
      103.77 -   138.36: 1
      138.36 -   172.95: 5
  Dihedral angle restraints: 5718
    sinusoidal: 2335
      harmonic: 3383
  Sorted by residual:
  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   49.07 -172.95     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C   1VU F5601 "
           pdb=" C1  1VU F5601 "
           pdb=" C2  1VU F5601 "
           pdb=" S   1VU F5601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.40 -131.00 -171.60     1      3.00e+01 1.11e-03 2.12e+01
  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  -73.52  159.61     1      3.00e+01 1.11e-03 2.07e+01
  ... (remaining 5715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 1406
       0.119 -    0.238: 21
       0.238 -    0.357: 0
       0.357 -    0.476: 0
       0.476 -    0.595: 1
  Chirality restraints: 1428
  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   -2.39   -0.60 2.00e-01 2.50e+01 8.86e+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    2.47    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE A 260 "
            pdb=" N   ILE A 260 "
            pdb=" C   ILE A 260 "
            pdb=" CB  ILE A 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.41e-01
  ... (remaining 1425 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 676 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.16e+00
        pdb=" N   PRO A 677 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 677 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 677 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 537 "    0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO B 538 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 538 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 538 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 664 "    0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO A 665 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 665 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 665 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 80
        2.57 -     3.15: 7405
        3.15 -     3.73: 13918
        3.73 -     4.32: 19695
        4.32 -     4.90: 33083
  Nonbonded interactions: 74181
  Sorted by model distance:
  nonbonded pdb=" O3B ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     1.982 2.170
  nonbonded pdb=" O1A ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.092 2.170
  nonbonded pdb=" OE1 GLU A 349 "
            pdb="MG    MG A 803 "
     model   vdw
     2.145 2.170
  nonbonded pdb=" O   VAL F 217 "
            pdb=" OG  SER F 221 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   HIS F  88 "
            pdb=" NZ  LYS F 101 "
     model   vdw
     2.187 3.120
  ... (remaining 74176 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:             3.750
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     9.810
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
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      :  0.011   0.607   9340  Z= 0.563
  Angle     :  1.029  56.014  12645  Z= 0.429
  Chirality :  0.049   0.595   1428
  Planarity :  0.004   0.051   1640
  Dihedral  : 15.778 172.954   3542
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  0.04 (0.25), residues: 1175
  helix:  0.70 (0.26), residues: 417
  sheet:  0.43 (0.32), residues: 248
  loop : -0.67 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 539 
 TYR   0.023   0.001   TYR A 473 
 PHE   0.014   0.001   PHE F 122 
 TRP   0.009   0.001   TRP A 394 
 HIS   0.007   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.01116 ( 9339)
  covalent geometry    : angle       1.02897 (12645)
  hydrogen bonds       : bond        0.14598 (  407)
  hydrogen bonds       : angle       5.81903 ( 1191)
  Misc. bond           : bond        0.12850 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.325 
Fit side-chains
REVERT: B  488 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8649 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.6114
  time to fit residues: 77.1093
Evaluate side-chains
  96 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0570
   chunk 65 optimal weight:   50.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.143094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.086443 restraints weight = 14101.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.30
r_work: 0.2853 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
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      :  0.003   0.035   9340  Z= 0.130
  Angle     :  0.571   7.494  12645  Z= 0.294
  Chirality :  0.045   0.160   1428
  Planarity :  0.004   0.049   1640
  Dihedral  : 13.321 150.102   1393
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.38 %
    Favored  : 90.50 %
  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:  0.14 (0.25), residues: 1175
  helix:  0.78 (0.26), residues: 437
  sheet:  0.48 (0.32), residues: 245
  loop : -0.66 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 432 
 TYR   0.010   0.001   TYR A 444 
 PHE   0.026   0.001   PHE A  63 
 TRP   0.004   0.001   TRP A 559 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9339)
  covalent geometry    : angle       0.57098 (12645)
  hydrogen bonds       : bond        0.04219 (  407)
  hydrogen bonds       : angle       4.62072 ( 1191)
  Misc. bond           : bond        0.00028 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.8966 (pmt100) cc_final: 0.8618 (pmt100)
REVERT: A  257 ARG cc_start: 0.9005 (mmm-85) cc_final: 0.8656 (mmm-85)
REVERT: A  693 MET cc_start: 0.5245 (OUTLIER) cc_final: 0.4643 (ptm)
REVERT: F   42 LYS cc_start: 0.7945 (mttt) cc_final: 0.7628 (mmtm)
REVERT: F   99 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8364 (ptpp)
  outliers start: 11
  outliers final: 2
  residues processed: 107
  average time/residue: 0.6608
  time to fit residues: 74.8848
Evaluate side-chains
  106 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 45 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 384 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.142280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.088956 restraints weight = 14033.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.56
r_work: 0.2769 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8965
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9340  Z= 0.207
  Angle     :  0.584   8.329  12645  Z= 0.304
  Chirality :  0.046   0.157   1428
  Planarity :  0.004   0.047   1640
  Dihedral  : 12.325 133.966   1393
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.32 %
    Favored  : 87.74 %
  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:  0.19 (0.24), residues: 1175
  helix:  0.84 (0.26), residues: 435
  sheet:  0.84 (0.34), residues: 215
  loop : -0.76 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 432 
 TYR   0.009   0.001   TYR B 417 
 PHE   0.015   0.002   PHE A 152 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.008   0.001   HIS A 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 9339)
  covalent geometry    : angle       0.58449 (12645)
  hydrogen bonds       : bond        0.04625 (  407)
  hydrogen bonds       : angle       4.50102 ( 1191)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.8980 (pmt100) cc_final: 0.8626 (pmt100)
REVERT: A  690 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7874 (mp)
REVERT: A  693 MET cc_start: 0.4662 (OUTLIER) cc_final: 0.4052 (ptm)
REVERT: B  499 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.7900 (mpp-170)
REVERT: B  537 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8739 (mm)
REVERT: F   87 GLU cc_start: 0.4636 (OUTLIER) cc_final: 0.3638 (mp0)
REVERT: F  171 GLU cc_start: 0.8366 (pm20) cc_final: 0.7972 (pm20)
  outliers start: 19
  outliers final: 7
  residues processed: 116
  average time/residue: 0.6790
  time to fit residues: 83.1665
Evaluate side-chains
  111 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 GLU
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain F residue   60 LYS
Chi-restraints excluded: chain F residue   87 GLU
Chi-restraints excluded: chain F residue  235 THR
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 109 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 63 optimal weight:   20.0000
   chunk 76 optimal weight:    0.5980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.141142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.083420 restraints weight = 14212.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.30
r_work: 0.2802 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   9340  Z= 0.203
  Angle     :  0.576   8.747  12645  Z= 0.299
  Chirality :  0.046   0.151   1428
  Planarity :  0.004   0.048   1640
  Dihedral  : 11.474 133.300   1393
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.07 %
    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:  0.22 (0.24), residues: 1175
  helix:  0.87 (0.26), residues: 436
  sheet:  0.88 (0.34), residues: 210
  loop : -0.74 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 268 
 TYR   0.010   0.001   TYR B 417 
 PHE   0.019   0.002   PHE A  63 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.012   0.001   HIS A 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 9339)
  covalent geometry    : angle       0.57604 (12645)
  hydrogen bonds       : bond        0.04469 (  407)
  hydrogen bonds       : angle       4.45258 ( 1191)
  Misc. bond           : bond        0.00045 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.8970 (pmt100) cc_final: 0.8605 (pmt100)
REVERT: A  690 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7994 (mp)
REVERT: A  693 MET cc_start: 0.4669 (OUTLIER) cc_final: 0.3953 (ptm)
REVERT: B  499 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.7928 (mpp-170)
REVERT: B  520 ASP cc_start: 0.9038 (t70) cc_final: 0.8726 (t0)
REVERT: B  537 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (mm)
REVERT: F   87 GLU cc_start: 0.4658 (pm20) cc_final: 0.3384 (mp0)
REVERT: F   92 ASP cc_start: 0.8613 (m-30) cc_final: 0.8346 (m-30)
REVERT: F  171 GLU cc_start: 0.8382 (pm20) cc_final: 0.7857 (pm20)
  outliers start: 15
  outliers final: 6
  residues processed: 113
  average time/residue: 0.6545
  time to fit residues: 78.4385
Evaluate side-chains
  109 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain F residue   60 LYS
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 17 optimal weight:    8.9990
   chunk 112 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   chunk 8 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 685 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.142663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.084651 restraints weight = 14206.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.31
r_work: 0.2807 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9340  Z= 0.178
  Angle     :  0.576   9.915  12645  Z= 0.295
  Chirality :  0.045   0.153   1428
  Planarity :  0.004   0.048   1640
  Dihedral  : 10.842 132.278   1393
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.79 %
    Favored  : 84.27 %
  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:  0.25 (0.25), residues: 1175
  helix:  0.93 (0.26), residues: 436
  sheet:  0.51 (0.32), residues: 239
  loop : -0.62 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 230 
 TYR   0.011   0.001   TYR B 417 
 PHE   0.024   0.001   PHE A 152 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 9339)
  covalent geometry    : angle       0.57623 (12645)
  hydrogen bonds       : bond        0.04221 (  407)
  hydrogen bonds       : angle       4.37024 ( 1191)
  Misc. bond           : bond        0.00039 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.8992 (pmt100) cc_final: 0.8657 (pmt100)
REVERT: A  690 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7977 (mp)
REVERT: A  693 MET cc_start: 0.4411 (OUTLIER) cc_final: 0.3964 (pmm)
REVERT: B  499 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.7937 (mpp-170)
REVERT: B  520 ASP cc_start: 0.9039 (t70) cc_final: 0.8736 (t0)
REVERT: B  537 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: F   87 GLU cc_start: 0.4614 (OUTLIER) cc_final: 0.3186 (mp0)
REVERT: F   92 ASP cc_start: 0.8614 (m-30) cc_final: 0.8341 (m-30)
REVERT: F  171 GLU cc_start: 0.8383 (pm20) cc_final: 0.7808 (pm20)
REVERT: F  232 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.7952 (tppt)
  outliers start: 19
  outliers final: 5
  residues processed: 111
  average time/residue: 0.6724
  time to fit residues: 79.1482
Evaluate side-chains
  107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain F residue   87 GLU
Chi-restraints excluded: chain F residue  232 LYS
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 685 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.140517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.082560 restraints weight = 14197.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 2.32
r_work: 0.2788 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8961
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   9340  Z= 0.233
  Angle     :  0.611  10.336  12645  Z= 0.314
  Chirality :  0.047   0.158   1428
  Planarity :  0.004   0.049   1640
  Dihedral  : 10.538 131.694   1393
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.91 %
    Favored  : 83.04 %
  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:  0.22 (0.24), residues: 1175
  helix:  0.88 (0.25), residues: 435
  sheet:  0.79 (0.34), residues: 218
  loop : -0.71 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 230 
 TYR   0.015   0.001   TYR B 417 
 PHE   0.018   0.002   PHE B 490 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.008   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 9339)
  covalent geometry    : angle       0.61145 (12645)
  hydrogen bonds       : bond        0.04659 (  407)
  hydrogen bonds       : angle       4.42753 ( 1191)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.9028 (pmt100) cc_final: 0.8705 (pmt100)
REVERT: A  693 MET cc_start: 0.4506 (OUTLIER) cc_final: 0.4118 (pmm)
REVERT: B  499 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.7964 (mpp-170)
REVERT: B  520 ASP cc_start: 0.9049 (t70) cc_final: 0.8741 (t0)
REVERT: B  537 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8780 (mm)
REVERT: F   87 GLU cc_start: 0.4686 (OUTLIER) cc_final: 0.2826 (mp0)
REVERT: F   92 ASP cc_start: 0.8640 (m-30) cc_final: 0.8363 (m-30)
REVERT: F  171 GLU cc_start: 0.8427 (pm20) cc_final: 0.7896 (mp0)
REVERT: F  232 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.7944 (tppt)
  outliers start: 20
  outliers final: 9
  residues processed: 114
  average time/residue: 0.6661
  time to fit residues: 80.3954
Evaluate side-chains
  109 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain F residue   87 GLU
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  232 LYS
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.142608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.087134 restraints weight = 14188.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.48
r_work: 0.2803 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8946
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9340  Z= 0.164
  Angle     :  0.586  10.500  12645  Z= 0.300
  Chirality :  0.045   0.147   1428
  Planarity :  0.004   0.049   1640
  Dihedral  : 10.097 130.792   1393
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.73 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.25), residues: 1175
  helix:  0.98 (0.26), residues: 436
  sheet:  0.49 (0.32), residues: 242
  loop : -0.61 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 154 
 TYR   0.013   0.001   TYR B 417 
 PHE   0.014   0.001   PHE A  63 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9339)
  covalent geometry    : angle       0.58639 (12645)
  hydrogen bonds       : bond        0.04053 (  407)
  hydrogen bonds       : angle       4.32150 ( 1191)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.9050 (pmt100) cc_final: 0.8742 (pmt100)
REVERT: A  516 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7892 (mpp)
REVERT: A  693 MET cc_start: 0.4377 (OUTLIER) cc_final: 0.3951 (pmm)
REVERT: B  499 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.7967 (mpp-170)
REVERT: B  520 ASP cc_start: 0.9063 (t70) cc_final: 0.8766 (t0)
REVERT: B  537 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8724 (mm)
REVERT: F   87 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.2841 (mp0)
REVERT: F   92 ASP cc_start: 0.8617 (m-30) cc_final: 0.8334 (m-30)
REVERT: F  171 GLU cc_start: 0.8441 (pm20) cc_final: 0.7904 (mp0)
REVERT: F  232 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.7947 (tppt)
  outliers start: 20
  outliers final: 12
  residues processed: 110
  average time/residue: 0.6196
  time to fit residues: 72.3179
Evaluate side-chains
  112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  693 MET
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  518 ASP
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain F residue   48 LEU
Chi-restraints excluded: chain F residue   60 LYS
Chi-restraints excluded: chain F residue   87 GLU
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  232 LYS
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 114 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.141983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.086772 restraints weight = 14116.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.47
r_work: 0.2807 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
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   0.040   9340  Z= 0.142
  Angle     :  0.577  11.499  12645  Z= 0.295
  Chirality :  0.044   0.146   1428
  Planarity :  0.004   0.049   1640
  Dihedral  :  9.818 130.176   1393
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.55 %
    Favored  : 81.61 %
  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: 1175
  helix:  1.04 (0.26), residues: 435
  sheet:  0.53 (0.32), residues: 242
  loop : -0.58 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 154 
 TYR   0.011   0.001   TYR B 417 
 PHE   0.019   0.001   PHE B 490 
 TRP   0.004   0.001   TRP A 559 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9339)
  covalent geometry    : angle       0.57730 (12645)
  hydrogen bonds       : bond        0.03842 (  407)
  hydrogen bonds       : angle       4.27060 ( 1191)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.9048 (pmt100) cc_final: 0.8744 (pmt100)
REVERT: A  628 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.9085 (tt0)
REVERT: B  499 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.7968 (mpp-170)
REVERT: B  520 ASP cc_start: 0.9056 (t70) cc_final: 0.8749 (OUTLIER)
REVERT: B  537 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8687 (mm)
REVERT: F   87 GLU cc_start: 0.4433 (OUTLIER) cc_final: 0.3084 (mp0)
REVERT: F  171 GLU cc_start: 0.8422 (pm20) cc_final: 0.7900 (mp0)
  outliers start: 18
  outliers final: 13
  residues processed: 109
  average time/residue: 0.6375
  time to fit residues: 73.8232
Evaluate side-chains
  109 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  628 GLN
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  518 ASP
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain F residue   48 LEU
Chi-restraints excluded: chain F residue   60 LYS
Chi-restraints excluded: chain F residue   87 GLU
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 116 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0570
   chunk 44 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.0106

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.141851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.088462 restraints weight = 14124.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.71
r_work: 0.2797 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9340  Z= 0.156
  Angle     :  0.601  12.842  12645  Z= 0.303
  Chirality :  0.045   0.157   1428
  Planarity :  0.004   0.049   1640
  Dihedral  :  9.650 129.806   1393
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.65 %
    Favored  : 81.41 %
  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:  0.33 (0.25), residues: 1175
  helix:  1.02 (0.26), residues: 435
  sheet:  0.54 (0.32), residues: 242
  loop : -0.58 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 154 
 TYR   0.012   0.001   TYR B 417 
 PHE   0.028   0.001   PHE A 263 
 TRP   0.004   0.001   TRP A 559 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9339)
  covalent geometry    : angle       0.60070 (12645)
  hydrogen bonds       : bond        0.03927 (  407)
  hydrogen bonds       : angle       4.27639 ( 1191)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.9068 (pmt100) cc_final: 0.8752 (pmt100)
REVERT: A  516 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7876 (mpp)
REVERT: A  628 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.9097 (tt0)
REVERT: B  499 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.7980 (mpp-170)
REVERT: B  520 ASP cc_start: 0.9068 (t70) cc_final: 0.8777 (OUTLIER)
REVERT: B  537 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8711 (mm)
REVERT: F   87 GLU cc_start: 0.4495 (OUTLIER) cc_final: 0.2950 (mp0)
REVERT: F   92 ASP cc_start: 0.8634 (m-30) cc_final: 0.8324 (m-30)
REVERT: F  171 GLU cc_start: 0.8449 (pm20) cc_final: 0.7914 (mp0)
  outliers start: 19
  outliers final: 12
  residues processed: 104
  average time/residue: 0.6815
  time to fit residues: 75.2648
Evaluate side-chains
  108 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  628 GLN
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain F residue   48 LEU
Chi-restraints excluded: chain F residue   60 LYS
Chi-restraints excluded: chain F residue   87 GLU
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 88 optimal weight:    0.1980
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    0.1980
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
B 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.143164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.089300 restraints weight = 14075.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.59
r_work: 0.2810 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8932
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9340  Z= 0.122
  Angle     :  0.593  12.880  12645  Z= 0.297
  Chirality :  0.044   0.153   1428
  Planarity :  0.004   0.050   1640
  Dihedral  :  9.404 129.153   1393
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 17.16 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.25), residues: 1175
  helix:  1.09 (0.26), residues: 437
  sheet:  0.59 (0.32), residues: 242
  loop : -0.52 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 154 
 TYR   0.009   0.001   TYR B 417 
 PHE   0.021   0.001   PHE A 263 
 TRP   0.004   0.001   TRP A 559 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9339)
  covalent geometry    : angle       0.59318 (12645)
  hydrogen bonds       : bond        0.03531 (  407)
  hydrogen bonds       : angle       4.20422 ( 1191)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ARG cc_start: 0.9042 (pmt100) cc_final: 0.8713 (pmt100)
REVERT: A  266 ASN cc_start: 0.8261 (t0) cc_final: 0.8055 (t0)
REVERT: A  516 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7893 (mpp)
REVERT: B  499 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.7956 (mpp-170)
REVERT: B  520 ASP cc_start: 0.9091 (t70) cc_final: 0.8797 (t0)
REVERT: F   87 GLU cc_start: 0.4328 (pm20) cc_final: 0.2996 (mp0)
REVERT: F  171 GLU cc_start: 0.8421 (pm20) cc_final: 0.7895 (mp0)
  outliers start: 15
  outliers final: 10
  residues processed: 106
  average time/residue: 0.6468
  time to fit residues: 72.6941
Evaluate side-chains
  106 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  169 HIS
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain B residue  518 ASP
Chi-restraints excluded: chain F residue   60 LYS
Chi-restraints excluded: chain F residue   95 MET
Chi-restraints excluded: chain F residue  248 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 62 optimal weight:   40.0000
   chunk 18 optimal weight:    8.9990
   chunk 89 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.142691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.085479 restraints weight = 14003.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 2.28
r_work: 0.2849 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9340  Z= 0.134
  Angle     :  0.607  12.972  12645  Z= 0.303
  Chirality :  0.044   0.156   1428
  Planarity :  0.004   0.048   1640
  Dihedral  :  9.347 129.132   1393
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 17.57 %
    Favored  : 81.21 %
  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:  0.45 (0.25), residues: 1175
  helix:  1.09 (0.26), residues: 437
  sheet:  0.61 (0.32), residues: 242
  loop : -0.51 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 154 
 TYR   0.011   0.001   TYR B 417 
 PHE   0.019   0.001   PHE A 263 
 TRP   0.004   0.001   TRP A 559 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9339)
  covalent geometry    : angle       0.60746 (12645)
  hydrogen bonds       : bond        0.03642 (  407)
  hydrogen bonds       : angle       4.19718 ( 1191)
  Misc. bond           : bond        0.00003 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3657.56 seconds
wall clock time: 62 minutes 57.70 seconds (3777.70 seconds total)