Starting phenix.real_space_refine
on Sun May  3 00:21:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uhr_64173/05_2026/9uhr_64173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uhr_64173/05_2026/9uhr_64173.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uhr_64173/05_2026/9uhr_64173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uhr_64173/05_2026/9uhr_64173.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uhr_64173/05_2026/9uhr_64173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uhr_64173/05_2026/9uhr_64173.map"
  }
  resolution = 2.48
  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=   0.014
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      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: 2.39, per 1000 atoms: 0.26
  Number of scatterers: 9172
  At special positions: 0
  Unit cell: (94.92, 99.12, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      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: 1.03
  Conformation dependent library (CDL) restraints added in 382.9 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:
      45 helices and 12 sheets defined
      39.4% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 85
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.604A  pdb=" N   ALA A  98 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 4.540A  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 123 through 135
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 4.015A  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 178 through 187
    Processing helix  chain 'A' and resid 201 through 212
      removed outlier: 3.768A  pdb=" N   ARG A 210 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   GLU A 211 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE A 212 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 252
      removed outlier: 3.776A  pdb=" N   ARG A 243 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 4.325A  pdb=" N   THR A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ILE A 364 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'A' and resid 385 through 389
    Processing helix  chain 'A' and resid 458 through 472
    Processing helix  chain 'A' and resid 481 through 490
      removed outlier: 3.545A  pdb=" N   ILE A 490 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 518 through 540
    Processing helix  chain 'A' and resid 641 through 648
      removed outlier: 3.674A  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: 3.907A  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 407
    Processing helix  chain 'B' and resid 407 through 422
      removed outlier: 3.656A  pdb=" N   ALA B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 442
      removed outlier: 3.829A  pdb=" N   ASP B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
      removed outlier: 3.552A  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
      removed outlier: 3.895A  pdb=" N   ALA B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 499
      removed outlier: 3.670A  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: 3.653A  pdb=" N   CYS B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 34 through 48
      removed outlier: 3.604A  pdb=" N   LEU F  48 " --> pdb=" O   ARG F  44 " (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 186
      removed outlier: 3.950A  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
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 3.903A  pdb=" N   ILE A  92 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232
    Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351
      removed outlier: 3.924A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   HIS A 269 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   GLU A 289 " --> pdb=" O   HIS A 269 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   GLU A 271 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLU A 287 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLN A 273 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   SER A 291 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   VAL A 300 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   GLN A 293 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LYS A 298 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 14.505A  pdb=" N   GLN A 297 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 10.841A  pdb=" N   TYR A 401 " --> pdb=" O   GLN A 297 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL A 299 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   TRP A 394 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   TYR A 455 " --> pdb=" O   TRP A 394 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL A 396 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ILE A 453 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   CYS A 398 " --> pdb=" O   LYS A 451 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LYS A 451 " --> pdb=" O   CYS A 398 " (cutoff:3.500A)
      removed outlier: 6.751A  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: 3.661A  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 559 through 565
      removed outlier: 6.657A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 662 through 663
      removed outlier: 7.774A  pdb=" N   LEU A 724 " --> pdb=" O   VAL A 710 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   VAL A 710 " --> pdb=" O   LEU A 724 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLU A 726 " --> pdb=" O   LYS A 708 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 695 through 698
      removed outlier: 6.639A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.532A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.532A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR B 451 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 82
      removed outlier: 4.519A  pdb=" N   THR F 109 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 8.558A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ARG F 259 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 199 through 201

    430 hydrogen bonds defined for protein.
    1185 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: 1.79

  Time building geometry restraints manager: 1.27 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: 2261
        1.42 -     1.56: 5413
        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  1.644  0.606 2.00e-02 2.50e+03 9.19e+02
  bond pdb=" C2  BTN A 801 "
       pdb=" S1  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.824  1.435  0.389 2.00e-02 2.50e+03 3.77e+02
  bond pdb=" O14 1VU F5601 "
       pdb=" P2  1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.682  1.467  0.215 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  1.361  0.199 2.00e-02 2.50e+03 9.93e+01
  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 9.45e+01
  ... (remaining 9334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.19: 12634
       11.19 -    22.38: 7
       22.38 -    33.56: 3
       33.56 -    44.75: 0
       44.75 -    55.94: 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  109.66  -55.94 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  108.85   31.36 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  109.65  -30.91 3.00e+00 1.11e-01 1.06e+02
  angle pdb=" O10 1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O7  1VU F5601 "
      ideal   model   delta    sigma   weight residual
      85.76  110.10  -24.34 3.00e+00 1.11e-01 6.59e+01
  angle pdb=" P   1VU F5601 "
        pdb=" O7  1VU F5601 "
        pdb=" P1  1VU F5601 "
      ideal   model   delta    sigma   weight residual
     143.93  123.45   20.48 3.00e+00 1.11e-01 4.66e+01
  ... (remaining 12640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.91: 5586
       34.91 -    69.81: 115
       69.81 -   104.72: 12
      104.72 -   139.62: 1
      139.62 -   174.53: 4
  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   50.65 -174.53     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 -129.23 -173.37     1      3.00e+01 1.11e-03 2.13e+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  -81.57  167.66     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 5715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 1411
       0.119 -    0.239: 16
       0.239 -    0.358: 0
       0.358 -    0.478: 0
       0.478 -    0.597: 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 8.91e+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 1.24e+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    2.60   -0.17 2.00e-01 2.50e+01 7.17e-01
  ... (remaining 1425 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 537 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.38e+00
        pdb=" N   PRO B 538 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 538 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 538 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 473 "   -0.013 2.00e-02 2.50e+03   1.02e-02 2.07e+00
        pdb=" CG  TYR A 473 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 473 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 473 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 473 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 473 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 473 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 473 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 489 "   -0.006 2.00e-02 2.50e+03   1.26e-02 1.59e+00
        pdb=" C   LYS B 489 "    0.022 2.00e-02 2.50e+03
        pdb=" O   LYS B 489 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   PHE B 490 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 118
        2.66 -     3.22: 8381
        3.22 -     3.78: 13861
        3.78 -     4.34: 19743
        4.34 -     4.90: 32391
  Nonbonded interactions: 74494
  Sorted by model distance:
  nonbonded pdb=" O2G ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.106 2.170
  nonbonded pdb=" O1A ATP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.122 2.170
  nonbonded pdb=" OE2 GLU A  73 "
            pdb=" OH  TYR A 143 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" NH1 ARG A  77 "
            pdb=" OG1 THR A  81 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OD1 ASP A 167 "
            pdb=" N   THR A 168 "
     model   vdw
     2.244 3.120
  ... (remaining 74489 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:             4.220
  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:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.880
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
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   0.606   9340  Z= 0.542
  Angle     :  0.967  55.941  12645  Z= 0.384
  Chirality :  0.047   0.597   1428
  Planarity :  0.003   0.063   1640
  Dihedral  : 15.405 174.531   3542
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.25), residues: 1175
  helix:  0.92 (0.27), residues: 423
  sheet:  0.65 (0.33), residues: 251
  loop : -0.46 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 135 
 TYR   0.024   0.001   TYR A 473 
 PHE   0.009   0.001   PHE B 490 
 TRP   0.009   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.01051 ( 9339)
  covalent geometry    : angle       0.96665 (12645)
  hydrogen bonds       : bond        0.14726 (  414)
  hydrogen bonds       : angle       5.50529 ( 1185)
  Misc. bond           : bond        0.12933 (    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
  127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.378 
Fit side-chains
REVERT: F   87 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7820 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.8530
  time to fit residues: 113.5091
Evaluate side-chains
  107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 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:
F 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.110341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.070221 restraints weight = 13181.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 2.30
r_work: 0.2644 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2523 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8977
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   9340  Z= 0.241
  Angle     :  0.590   7.409  12645  Z= 0.311
  Chirality :  0.048   0.173   1428
  Planarity :  0.004   0.065   1640
  Dihedral  : 14.042 159.179   1393
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.25 %
    Favored  : 91.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.24), residues: 1175
  helix:  1.00 (0.26), residues: 431
  sheet:  0.46 (0.32), residues: 255
  loop : -0.57 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 207 
 TYR   0.018   0.002   TYR A 473 
 PHE   0.016   0.002   PHE B 384 
 TRP   0.013   0.002   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 9339)
  covalent geometry    : angle       0.58959 (12645)
  hydrogen bonds       : bond        0.05407 (  414)
  hydrogen bonds       : angle       4.52313 ( 1185)
  Misc. bond           : bond        0.00203 (    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
  124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  217 MET cc_start: 0.8199 (tpt) cc_final: 0.7438 (tpt)
REVERT: F  143 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8443 (ttpt)
  outliers start: 11
  outliers final: 3
  residues processed: 118
  average time/residue: 0.8384
  time to fit residues: 103.6639
Evaluate side-chains
  108 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  556 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 113 optimal weight:    0.0470
   chunk 63 optimal weight:    6.9990
   chunk 11 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 114 optimal weight:    0.2980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.113446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.073833 restraints weight = 13089.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 2.26
r_work: 0.2713 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2593 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8928
moved from start:          0.1149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9340  Z= 0.104
  Angle     :  0.500   6.409  12645  Z= 0.261
  Chirality :  0.044   0.161   1428
  Planarity :  0.004   0.065   1640
  Dihedral  : 12.588 157.747   1393
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.99 %
    Favored  : 89.99 %
  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:  0.55 (0.25), residues: 1175
  helix:  1.25 (0.26), residues: 431
  sheet:  0.64 (0.33), residues: 244
  loop : -0.50 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 390 
 TYR   0.009   0.001   TYR F 206 
 PHE   0.013   0.001   PHE A 242 
 TRP   0.010   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9339)
  covalent geometry    : angle       0.50040 (12645)
  hydrogen bonds       : bond        0.03795 (  414)
  hydrogen bonds       : angle       4.23182 ( 1185)
  Misc. bond           : bond        0.00017 (    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
  125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8532 (tp30) cc_final: 0.8299 (tp30)
REVERT: A  217 MET cc_start: 0.7912 (tpt) cc_final: 0.7417 (tpt)
REVERT: A  584 GLU cc_start: 0.8780 (tp30) cc_final: 0.8432 (tm-30)
REVERT: B  489 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8665 (ttpp)
REVERT: B  490 PHE cc_start: 0.7662 (m-80) cc_final: 0.7080 (m-10)
  outliers start: 10
  outliers final: 4
  residues processed: 121
  average time/residue: 0.8010
  time to fit residues: 101.9104
Evaluate side-chains
  112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain F residue  229 ASP
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:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 101 optimal weight:    3.9990
   chunk 8 optimal weight:    0.2980
   chunk 89 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
B 492 ASN

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 = 0.112482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.073378 restraints weight = 13232.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 2.26
r_work: 0.2702 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2582 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8932
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9340  Z= 0.113
  Angle     :  0.487   6.434  12645  Z= 0.256
  Chirality :  0.044   0.161   1428
  Planarity :  0.003   0.064   1640
  Dihedral  : 11.712 157.209   1393
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.60 %
    Favored  : 88.76 %
  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:  0.61 (0.25), residues: 1175
  helix:  1.33 (0.26), residues: 431
  sheet:  0.65 (0.33), residues: 244
  loop : -0.48 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 207 
 TYR   0.009   0.001   TYR F 120 
 PHE   0.014   0.001   PHE A 242 
 TRP   0.010   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9339)
  covalent geometry    : angle       0.48661 (12645)
  hydrogen bonds       : bond        0.03805 (  414)
  hydrogen bonds       : angle       4.14484 ( 1185)
  Misc. bond           : bond        0.00032 (    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
  132 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8577 (tp30) cc_final: 0.8288 (tp30)
REVERT: A  182 LEU cc_start: 0.9521 (mp) cc_final: 0.9290 (mm)
REVERT: A  217 MET cc_start: 0.7937 (tpt) cc_final: 0.7634 (tpt)
REVERT: A  584 GLU cc_start: 0.8798 (tp30) cc_final: 0.8487 (tm-30)
REVERT: A  652 GLU cc_start: 0.8249 (tp30) cc_final: 0.8047 (OUTLIER)
REVERT: B  360 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8833 (mtmt)
REVERT: B  489 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8789 (ttpp)
REVERT: F  238 ASP cc_start: 0.8675 (m-30) cc_final: 0.8470 (m-30)
  outliers start: 16
  outliers final: 9
  residues processed: 128
  average time/residue: 0.8071
  time to fit residues: 108.6092
Evaluate side-chains
  121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  520 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  229 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 112 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.111677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.072219 restraints weight = 13211.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 2.24
r_work: 0.2681 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9340  Z= 0.145
  Angle     :  0.504   6.248  12645  Z= 0.267
  Chirality :  0.045   0.173   1428
  Planarity :  0.004   0.065   1640
  Dihedral  : 11.370 156.474   1393
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.42 %
    Favored  : 88.25 %
  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:  0.57 (0.25), residues: 1175
  helix:  1.31 (0.26), residues: 431
  sheet:  0.57 (0.33), residues: 246
  loop : -0.48 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 207 
 TYR   0.010   0.001   TYR F 206 
 PHE   0.016   0.001   PHE A 242 
 TRP   0.010   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9339)
  covalent geometry    : angle       0.50373 (12645)
  hydrogen bonds       : bond        0.04155 (  414)
  hydrogen bonds       : angle       4.16096 ( 1185)
  Misc. bond           : bond        0.00030 (    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
  126 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8569 (tp30) cc_final: 0.8251 (tp30)
REVERT: A  182 LEU cc_start: 0.9545 (mp) cc_final: 0.9286 (mm)
REVERT: A  584 GLU cc_start: 0.8773 (tp30) cc_final: 0.8459 (tm-30)
REVERT: B  360 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8871 (mtmt)
REVERT: B  489 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8802 (ttpp)
  outliers start: 13
  outliers final: 8
  residues processed: 123
  average time/residue: 0.8616
  time to fit residues: 111.0922
Evaluate side-chains
  120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  376 ARG
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  229 ASP
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:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 37 optimal weight:    0.4980
   chunk 44 optimal weight:    0.0470
   chunk 109 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.5078

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.113008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.073542 restraints weight = 13236.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.25
r_work: 0.2706 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2586 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9340  Z= 0.104
  Angle     :  0.484   6.057  12645  Z= 0.256
  Chirality :  0.044   0.172   1428
  Planarity :  0.004   0.064   1640
  Dihedral  : 11.005 155.198   1393
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.44 %
    Favored  : 87.13 %
  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:  0.67 (0.25), residues: 1175
  helix:  1.38 (0.26), residues: 432
  sheet:  0.66 (0.33), residues: 244
  loop : -0.44 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 390 
 TYR   0.009   0.001   TYR F 206 
 PHE   0.020   0.001   PHE A 242 
 TRP   0.010   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 9339)
  covalent geometry    : angle       0.48432 (12645)
  hydrogen bonds       : bond        0.03544 (  414)
  hydrogen bonds       : angle       4.05736 ( 1185)
  Misc. bond           : bond        0.00016 (    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
  127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8555 (tp30) cc_final: 0.8208 (tp30)
REVERT: A  584 GLU cc_start: 0.8777 (tp30) cc_final: 0.8435 (tm-30)
REVERT: B  360 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8851 (mtmt)
REVERT: B  489 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8799 (ttpp)
  outliers start: 14
  outliers final: 8
  residues processed: 123
  average time/residue: 0.8462
  time to fit residues: 109.2911
Evaluate side-chains
  120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  229 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 71 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.111184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.071134 restraints weight = 13229.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.2788 rms_B_bonded: 2.28
r_work: 0.2658 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8967
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9340  Z= 0.168
  Angle     :  0.531   6.478  12645  Z= 0.281
  Chirality :  0.045   0.162   1428
  Planarity :  0.004   0.064   1640
  Dihedral  : 10.994 154.217   1393
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.64 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1175
  helix:  1.29 (0.26), residues: 432
  sheet:  0.54 (0.33), residues: 246
  loop : -0.46 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 207 
 TYR   0.010   0.001   TYR F 206 
 PHE   0.020   0.001   PHE A 242 
 TRP   0.010   0.001   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9339)
  covalent geometry    : angle       0.53055 (12645)
  hydrogen bonds       : bond        0.04474 (  414)
  hydrogen bonds       : angle       4.17407 ( 1185)
  Misc. bond           : bond        0.00002 (    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
  126 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8604 (tp30) cc_final: 0.8261 (tp30)
REVERT: A  182 LEU cc_start: 0.9563 (mp) cc_final: 0.9314 (mm)
REVERT: A  584 GLU cc_start: 0.8738 (tp30) cc_final: 0.8469 (tm-30)
REVERT: B  360 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8834 (mtmt)
REVERT: B  489 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8810 (ttpp)
REVERT: F   38 ARG cc_start: 0.3673 (OUTLIER) cc_final: 0.1500 (ttt180)
  outliers start: 15
  outliers final: 9
  residues processed: 122
  average time/residue: 0.8389
  time to fit residues: 107.4464
Evaluate side-chains
  119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain B residue  376 ARG
Chi-restraints excluded: chain F residue   38 ARG
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  229 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 88 optimal weight:    0.1980
   chunk 114 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0670
   chunk 16 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.112464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.073006 restraints weight = 13157.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.28
r_work: 0.2698 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2579 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8934
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9340  Z= 0.114
  Angle     :  0.501   6.400  12645  Z= 0.265
  Chirality :  0.044   0.166   1428
  Planarity :  0.004   0.065   1640
  Dihedral  : 10.766 153.462   1393
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.85 %
    Favored  : 86.72 %
  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:  0.66 (0.25), residues: 1175
  helix:  1.38 (0.26), residues: 432
  sheet:  0.63 (0.33), residues: 244
  loop : -0.44 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 207 
 TYR   0.009   0.001   TYR F 206 
 PHE   0.019   0.001   PHE A 242 
 TRP   0.011   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9339)
  covalent geometry    : angle       0.50142 (12645)
  hydrogen bonds       : bond        0.03646 (  414)
  hydrogen bonds       : angle       4.08174 ( 1185)
  Misc. bond           : bond        0.00025 (    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
  126 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 GLU cc_start: 0.8566 (tp30) cc_final: 0.8200 (tp30)
REVERT: A  182 LEU cc_start: 0.9556 (mp) cc_final: 0.9290 (mm)
REVERT: A  448 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8981 (ttp)
REVERT: A  584 GLU cc_start: 0.8740 (tp30) cc_final: 0.8479 (tm-30)
REVERT: B  360 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8863 (mtmt)
REVERT: B  489 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8839 (ttpp)
REVERT: F   38 ARG cc_start: 0.3725 (OUTLIER) cc_final: 0.1501 (ttt180)
  outliers start: 14
  outliers final: 7
  residues processed: 122
  average time/residue: 0.8285
  time to fit residues: 106.3185
Evaluate side-chains
  120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain F residue   38 ARG
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  229 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 116 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 44 optimal weight:    0.1980
   chunk 104 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.112680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.073031 restraints weight = 13165.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 2.28
r_work: 0.2689 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9340  Z= 0.117
  Angle     :  0.503   6.179  12645  Z= 0.266
  Chirality :  0.044   0.163   1428
  Planarity :  0.004   0.064   1640
  Dihedral  : 10.674 152.727   1393
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.05 %
    Favored  : 86.72 %
  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:  0.67 (0.25), residues: 1175
  helix:  1.41 (0.26), residues: 432
  sheet:  0.65 (0.33), residues: 244
  loop : -0.46 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 207 
 TYR   0.009   0.001   TYR F 206 
 PHE   0.019   0.001   PHE A 242 
 TRP   0.010   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9339)
  covalent geometry    : angle       0.50269 (12645)
  hydrogen bonds       : bond        0.03698 (  414)
  hydrogen bonds       : angle       4.06161 ( 1185)
  Misc. bond           : bond        0.00026 (    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
  119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8564 (tp30) cc_final: 0.8195 (tp30)
REVERT: A  448 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8998 (ttp)
REVERT: A  584 GLU cc_start: 0.8737 (tp30) cc_final: 0.8471 (tm-30)
REVERT: B  360 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8868 (mtmt)
REVERT: B  489 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8755 (ttpp)
REVERT: F   38 ARG cc_start: 0.3753 (OUTLIER) cc_final: 0.1525 (ttt180)
REVERT: F   87 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8018 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 115
  average time/residue: 0.8280
  time to fit residues: 100.0120
Evaluate side-chains
  118 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain F residue   38 ARG
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0470
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.3684

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.110787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.070923 restraints weight = 13193.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.23
r_work: 0.2654 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2534 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8969
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9340  Z= 0.189
  Angle     :  0.556   8.214  12645  Z= 0.292
  Chirality :  0.046   0.162   1428
  Planarity :  0.004   0.064   1640
  Dihedral  : 10.757 152.660   1393
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.36 %
    Favored  : 86.31 %
  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:  0.55 (0.25), residues: 1175
  helix:  1.31 (0.26), residues: 432
  sheet:  0.58 (0.33), residues: 254
  loop : -0.56 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 207 
 TYR   0.011   0.001   TYR F 206 
 PHE   0.028   0.002   PHE A 242 
 TRP   0.009   0.001   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 9339)
  covalent geometry    : angle       0.55556 (12645)
  hydrogen bonds       : bond        0.04518 (  414)
  hydrogen bonds       : angle       4.16864 ( 1185)
  Misc. bond           : bond        0.00022 (    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
  123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.8598 (tp30) cc_final: 0.8262 (tp30)
REVERT: A  182 LEU cc_start: 0.9557 (mp) cc_final: 0.9351 (mm)
REVERT: A  448 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9078 (ttp)
REVERT: A  584 GLU cc_start: 0.8735 (tp30) cc_final: 0.8468 (tm-30)
REVERT: A  652 GLU cc_start: 0.8346 (tp30) cc_final: 0.8086 (tp30)
REVERT: B  360 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8851 (mtmt)
REVERT: B  489 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8622 (ttpp)
REVERT: F   38 ARG cc_start: 0.3625 (OUTLIER) cc_final: 0.1451 (ttt180)
REVERT: F   87 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8026 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 117
  average time/residue: 0.8466
  time to fit residues: 103.9196
Evaluate side-chains
  122 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  360 LYS
Chi-restraints excluded: chain F residue   38 ARG
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  168 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 88 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 696 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.111667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.072078 restraints weight = 13052.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 2.25
r_work: 0.2675 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2556 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9340  Z= 0.139
  Angle     :  0.523   7.603  12645  Z= 0.276
  Chirality :  0.045   0.164   1428
  Planarity :  0.004   0.065   1640
  Dihedral  : 10.651 152.323   1393
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.26 %
    Favored  : 86.41 %
  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:  0.57 (0.25), residues: 1175
  helix:  1.34 (0.26), residues: 432
  sheet:  0.61 (0.34), residues: 243
  loop : -0.54 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 207 
 TYR   0.010   0.001   TYR F 206 
 PHE   0.017   0.001   PHE A 242 
 TRP   0.011   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9339)
  covalent geometry    : angle       0.52314 (12645)
  hydrogen bonds       : bond        0.04040 (  414)
  hydrogen bonds       : angle       4.12937 ( 1185)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4655.29 seconds
wall clock time: 79 minutes 49.78 seconds (4789.78 seconds total)