Starting phenix.real_space_refine
on Sun May  3 00:26:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uh5_64155/05_2026/9uh5_64155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uh5_64155/05_2026/9uh5_64155.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uh5_64155/05_2026/9uh5_64155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uh5_64155/05_2026/9uh5_64155.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uh5_64155/05_2026/9uh5_64155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uh5_64155/05_2026/9uh5_64155.map"
  }
  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       5      5.49       5
     Mg      1      5.21       5
     S      53      5.16       5
     C    5754      2.51       5
     N    1604      2.21       5
     O    1751      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: 9168
  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: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 47
          Unusual residues: {' MG': 1, 'ADP': 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: 2.32, per 1000 atoms: 0.25
  Number of scatterers: 9168
  At special positions: 0
  Unit cell: (96.05, 100.3, 137.7, 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       5     15.00
     Mg      1     11.99
     O    1751      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: 0.91
  Conformation dependent library (CDL) restraints added in 341.4 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 15 sheets defined
      39.1% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 85
    Processing helix  chain 'A' and resid 95 through 100
      removed outlier: 4.252A  pdb=" N   SER A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 106
      removed outlier: 3.539A  pdb=" N   ALA A 106 " --> pdb=" O   HIS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 135
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.602A  pdb=" N   ALA A 153 " --> pdb=" O   ASN A 149 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ARG A 154 " --> pdb=" O   LYS A 150 " (cutoff:3.500A)
      removed outlier: 4.412A  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
      removed outlier: 3.767A  pdb=" N   LEU A 182 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 213
      removed outlier: 3.956A  pdb=" N   GLU A 211 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLY A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 251
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 357 through 363
      removed outlier: 4.349A  pdb=" N   THR A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU A 362 " --> pdb=" O   HIS A 358 " (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
      removed outlier: 3.706A  pdb=" N   ASP A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN A 472 " --> pdb=" O   ASP A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 490
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 3.541A  pdb=" N   ASP A 506 " --> pdb=" O   LYS A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 540
    Processing helix  chain 'A' and resid 641 through 648
      removed outlier: 3.784A  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: 3.985A  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: 3.544A  pdb=" N   VAL B 372 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 406
    Processing helix  chain 'B' and resid 407 through 421
      removed outlier: 3.663A  pdb=" N   HIS B 411 " --> pdb=" O   GLY B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 442
    Processing helix  chain 'B' and resid 464 through 473
    Processing helix  chain 'B' and resid 479 through 490
      removed outlier: 3.607A  pdb=" N   ALA B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 499
      removed outlier: 3.558A  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: 3.913A  pdb=" N   CYS B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP B 518 " --> pdb=" O   ARG B 514 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 34 through 49
      removed outlier: 3.563A  pdb=" N   ARG F  38 " --> pdb=" O   SER F  34 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE F  39 " --> pdb=" O   VAL F  35 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 61
      removed outlier: 3.687A  pdb=" N   ARG F  61 " --> pdb=" O   ALA F  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 97 through 101
      removed outlier: 3.570A  pdb=" N   ASN F 100 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 105
      removed outlier: 3.563A  pdb=" N   ASP F 105 " --> pdb=" O   PHE F 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 102 through 105'
    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: 3.754A  pdb=" N   LEU F 173 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY F 175 " --> pdb=" O   GLU F 171 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TYR F 176 " --> pdb=" O   SER F 172 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG F 182 " --> pdb=" O   ASP F 178 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 210
      removed outlier: 3.761A  pdb=" N   ALA F 209 " --> pdb=" O   VAL F 205 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 227 through 236
    Processing helix  chain 'F' and resid 240 through 246
    Processing helix  chain 'F' and resid 246 through 253
    Processing helix  chain 'F' and resid 263 through 278
      removed outlier: 3.685A  pdb=" N   ASP F 273 " --> pdb=" O   CYS F 269 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU F 278 " --> pdb=" O   PHE F 274 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.328A  pdb=" N   ILE A  66 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ILE A  92 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   VAL A  68 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   HIS A 140 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU A  67 " --> pdb=" O   HIS A 140 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 162 " (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 282 through 289
      removed outlier: 4.586A  pdb=" N   GLN A 273 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU A 287 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU A 271 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   GLU A 289 " --> pdb=" O   HIS A 269 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   HIS A 269 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 294
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 404
    Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416
      removed outlier: 4.171A  pdb=" N   GLY A 415 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 421
    Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 565
      removed outlier: 6.622A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 695 through 698
      removed outlier: 6.848A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 707 through 710
      removed outlier: 7.197A  pdb=" N   GLU A 726 " --> pdb=" O   LYS A 708 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.640A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU B 459 " --> pdb=" O   ILE B 430 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ARG B 432 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ALA B 461 " --> pdb=" O   ARG B 432 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ALA B 434 " --> pdb=" O   ALA B 461 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.640A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   ILE B 389 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   GLY B 353 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   PHE B 391 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   VAL B 355 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ASP B 393 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   ASN B 357 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR B 451 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA B 454 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 80 through 81
      removed outlier: 8.675A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE F 213 " --> pdb=" O   GLN F 192 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL F 217 " --> pdb=" O   ILE F 196 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   THR F 214 " --> pdb=" O   ARG F 259 " (cutoff:3.500A)
      removed outlier: 8.639A  pdb=" N   PHE F 261 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   MET F 216 " --> pdb=" O   PHE F 261 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 199 through 201
      removed outlier: 5.712A  pdb=" N   TYR F 222 " --> pdb=" O   CYS F 200 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6

    401 hydrogen bonds defined for protein.
    1101 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: 1.52

  Time building geometry restraints manager: 1.06 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: 1561
        1.28 -     1.42: 2261
        1.42 -     1.56: 5408
        1.56 -     1.70: 19
        1.70 -     1.84: 86
  Bond restraints: 9335
  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 9.18e+02
  bond pdb=" C2  BTN A 801 "
       pdb=" S1  BTN A 801 "
    ideal  model  delta    sigma   weight residual
    1.824  1.432  0.392 2.00e-02 2.50e+03 3.84e+02
  bond pdb=" C2' ADP A 802 "
       pdb=" C3' ADP A 802 "
    ideal  model  delta    sigma   weight residual
    1.524  1.245  0.279 2.00e-02 2.50e+03 1.94e+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  1.362  0.198 2.00e-02 2.50e+03 9.84e+01
  ... (remaining 9330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.20: 12623
       11.20 -    22.39: 9
       22.39 -    33.59: 5
       33.59 -    44.79: 0
       44.79 -    55.98: 1
  Bond angle restraints: 12638
  Sorted by residual:
  angle pdb=" O14 1VU F5601 "
        pdb=" P2  1VU F5601 "
        pdb=" O15 1VU F5601 "
      ideal   model   delta    sigma   weight residual
      53.72  109.70  -55.98 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  109.05   31.16 3.00e+00 1.11e-01 1.08e+02
  angle pdb=" O10 1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O9  1VU F5601 "
      ideal   model   delta    sigma   weight residual
      78.74  109.25  -30.51 3.00e+00 1.11e-01 1.03e+02
  angle pdb=" C1' ADP A 802 "
        pdb=" N9  ADP A 802 "
        pdb=" C4  ADP A 802 "
      ideal   model   delta    sigma   weight residual
     126.00  153.36  -27.36 3.00e+00 1.11e-01 8.32e+01
  angle pdb=" C1' ADP A 802 "
        pdb=" N9  ADP A 802 "
        pdb=" C8  ADP A 802 "
      ideal   model   delta    sigma   weight residual
     126.00   99.37   26.63 3.00e+00 1.11e-01 7.88e+01
  ... (remaining 12633 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.49: 5577
       34.49 -    68.99: 99
       68.99 -   103.48: 13
      103.48 -   137.97: 1
      137.97 -   172.47: 5
  Dihedral angle restraints: 5695
    sinusoidal: 2312
      harmonic: 3383
  Sorted by residual:
  dihedral pdb=" C5' ADP A 802 "
           pdb=" O5' ADP A 802 "
           pdb=" PA  ADP A 802 "
           pdb=" O2A ADP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   71.24 -131.23     1      2.00e+01 2.50e-03 3.98e+01
  dihedral pdb=" O1B ADP A 802 "
           pdb=" O3A ADP A 802 "
           pdb=" PB  ADP A 802 "
           pdb=" PA  ADP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   34.10  -94.11     1      2.00e+01 2.50e-03 2.57e+01
  dihedral pdb=" C   1VU F5601 "
           pdb=" C1  1VU F5601 "
           pdb=" C2  1VU F5601 "
           pdb=" O   1VU F5601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -123.88   48.59 -172.47     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 5692 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 1414
       0.121 -    0.242: 13
       0.242 -    0.364: 0
       0.364 -    0.485: 0
       0.485 -    0.606: 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   -2.38   -0.61 2.00e-01 2.50e+01 9.18e+00
  chirality pdb=" C16 1VU F5601 "
            pdb=" C22 1VU F5601 "
            pdb=" N2  1VU F5601 "
            pdb=" O11 1VU F5601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.48    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE A 231 "
            pdb=" N   ILE A 231 "
            pdb=" C   ILE A 231 "
            pdb=" CB  ILE A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.10e-01
  ... (remaining 1425 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 233 "    0.019 2.00e-02 2.50e+03   1.57e-02 6.12e+00
        pdb=" CG  TRP A 233 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 233 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 233 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 233 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 233 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 233 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 233 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 233 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 233 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 537 "   -0.041 5.00e-02 4.00e+02   6.17e-02 6.09e+00
        pdb=" N   PRO B 538 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B 538 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 538 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 436 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO A 437 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 192
        2.70 -     3.25: 8662
        3.25 -     3.80: 13515
        3.80 -     4.35: 18160
        4.35 -     4.90: 30645
  Nonbonded interactions: 71174
  Sorted by model distance:
  nonbonded pdb=" O2A ADP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.145 2.170
  nonbonded pdb=" O1B ADP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.181 2.170
  nonbonded pdb=" O3B ADP A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.192 2.170
  nonbonded pdb=" C8  ADP A 802 "
            pdb=" O4' ADP A 802 "
     model   vdw
     2.201 2.608
  nonbonded pdb=" OD2 ASP F 105 "
            pdb=" OG  SER F 134 "
     model   vdw
     2.206 3.040
  ... (remaining 71169 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.610
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.360
  Find NCS groups from input model:        0.040
  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:7.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
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      :  0.012   0.606   9336  Z= 0.595
  Angle     :  1.061  55.983  12638  Z= 0.407
  Chirality :  0.047   0.606   1428
  Planarity :  0.003   0.062   1640
  Dihedral  : 15.311 172.469   3519
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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:  0.90 (0.28), residues: 401
  sheet:  1.57 (0.35), residues: 216
  loop : -0.81 (0.27), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 641 
 TYR   0.013   0.001   TYR F 277 
 PHE   0.010   0.001   PHE F 122 
 TRP   0.041   0.002   TRP A 233 
 HIS   0.006   0.001   HIS F  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.01158 ( 9335)
  covalent geometry    : angle       1.06104 (12638)
  hydrogen bonds       : bond        0.15152 (  385)
  hydrogen bonds       : angle       5.88796 ( 1101)
  Misc. bond           : bond        0.13200 (    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
  133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  217 MET cc_start: 0.7482 (tpt) cc_final: 0.7185 (tpp)
REVERT: A  666 MET cc_start: 0.9249 (ptm) cc_final: 0.9023 (ptp)
REVERT: B  459 GLU cc_start: 0.7956 (pp20) cc_final: 0.7748 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.5817
  time to fit residues: 82.4500
Evaluate side-chains
  97 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    1.6184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.122884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.076730 restraints weight = 15194.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.93
r_work: 0.2787 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9336  Z= 0.214
  Angle     :  0.599   7.169  12638  Z= 0.305
  Chirality :  0.048   0.193   1428
  Planarity :  0.004   0.055   1640
  Dihedral  : 12.843 165.825   1370
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  8.27 %
    Favored  : 89.68 %
  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 (0.25), residues: 1175
  helix:  0.84 (0.26), residues: 421
  sheet:  1.13 (0.35), residues: 232
  loop : -0.87 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 154 
 TYR   0.024   0.001   TYR A 473 
 PHE   0.018   0.002   PHE A 152 
 TRP   0.019   0.002   TRP A 233 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 9335)
  covalent geometry    : angle       0.59859 (12638)
  hydrogen bonds       : bond        0.05036 (  385)
  hydrogen bonds       : angle       4.48215 ( 1101)
  Misc. bond           : bond        0.00002 (    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
  125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.335 
Fit side-chains
REVERT: B  459 GLU cc_start: 0.8332 (pp20) cc_final: 0.7902 (pp20)
REVERT: F   61 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8530 (mtt180)
REVERT: F  139 GLN cc_start: 0.8741 (tt0) cc_final: 0.8530 (tt0)
  outliers start: 20
  outliers final: 10
  residues processed: 116
  average time/residue: 0.5363
  time to fit residues: 66.7609
Evaluate side-chains
  114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain F residue   65 THR
Chi-restraints excluded: chain F residue  147 GLN
Chi-restraints excluded: chain F residue  151 VAL
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  291 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
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 = 0.3669 r_free = 0.3669 target = 0.121609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.075535 restraints weight = 15141.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 2.92
r_work: 0.2766 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   9336  Z= 0.233
  Angle     :  0.588   7.102  12638  Z= 0.303
  Chirality :  0.048   0.209   1428
  Planarity :  0.004   0.054   1640
  Dihedral  : 11.913 169.685   1370
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.44 %
    Favored  : 86.01 %
  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:  0.12 (0.25), residues: 1175
  helix:  0.80 (0.26), residues: 424
  sheet:  1.00 (0.34), residues: 232
  loop : -0.94 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 154 
 TYR   0.027   0.002   TYR A 473 
 PHE   0.015   0.002   PHE F 122 
 TRP   0.010   0.001   TRP A 394 
 HIS   0.004   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 ( 9335)
  covalent geometry    : angle       0.58822 (12638)
  hydrogen bonds       : bond        0.04962 (  385)
  hydrogen bonds       : angle       4.33622 ( 1101)
  Misc. bond           : bond        0.00005 (    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
  127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  217 MET cc_start: 0.7699 (tpp) cc_final: 0.7402 (tpp)
REVERT: B  459 GLU cc_start: 0.8357 (pp20) cc_final: 0.7769 (pp20)
REVERT: F   59 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.6135 (m-70)
REVERT: F  139 GLN cc_start: 0.8731 (tt0) cc_final: 0.8507 (tt0)
  outliers start: 25
  outliers final: 13
  residues processed: 117
  average time/residue: 0.5264
  time to fit residues: 66.2918
Evaluate side-chains
  118 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain F residue   59 HIS
Chi-restraints excluded: chain F residue  147 GLN
Chi-restraints excluded: chain F residue  151 VAL
Chi-restraints excluded: chain F residue  235 THR
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  291 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0000
   chunk 76 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9990
   chunk 112 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.1388

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.122572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.077128 restraints weight = 15209.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.89
r_work: 0.2790 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9336  Z= 0.158
  Angle     :  0.547   6.862  12638  Z= 0.279
  Chirality :  0.046   0.175   1428
  Planarity :  0.004   0.053   1640
  Dihedral  : 11.250 170.458   1370
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.36 %
    Favored  : 85.19 %
  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:  0.98 (0.26), residues: 421
  sheet:  1.04 (0.34), residues: 230
  loop : -0.90 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 154 
 TYR   0.015   0.001   TYR A 473 
 PHE   0.011   0.001   PHE A 533 
 TRP   0.006   0.001   TRP A 284 
 HIS   0.005   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9335)
  covalent geometry    : angle       0.54655 (12638)
  hydrogen bonds       : bond        0.04113 (  385)
  hydrogen bonds       : angle       4.14169 ( 1101)
  Misc. bond           : bond        0.00028 (    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
  127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.357 
Fit side-chains
REVERT: B  459 GLU cc_start: 0.8318 (pp20) cc_final: 0.7785 (pp20)
REVERT: B  494 PHE cc_start: 0.8169 (m-80) cc_final: 0.7713 (m-80)
REVERT: F   59 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6021 (m-70)
  outliers start: 24
  outliers final: 15
  residues processed: 121
  average time/residue: 0.5238
  time to fit residues: 68.2915
Evaluate side-chains
  116 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain F residue   59 HIS
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  235 THR
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  291 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0070
   chunk 52 optimal weight:    0.6980
   chunk 105 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0980
   chunk 115 optimal weight:    0.0070
   chunk 107 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.3416

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

Flipped N/Q/H residues before XYZ refinement:
B 348 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.125833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.080188 restraints weight = 15182.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.95
r_work: 0.2852 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9336  Z= 0.091
  Angle     :  0.509   6.990  12638  Z= 0.255
  Chirality :  0.044   0.143   1428
  Planarity :  0.003   0.054   1640
  Dihedral  : 10.680 169.630   1370
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.79 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.25), residues: 1175
  helix:  1.15 (0.26), residues: 424
  sheet:  1.28 (0.35), residues: 223
  loop : -0.78 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  61 
 TYR   0.021   0.001   TYR B 417 
 PHE   0.010   0.001   PHE A 152 
 TRP   0.006   0.001   TRP A 284 
 HIS   0.003   0.000   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 9335)
  covalent geometry    : angle       0.50947 (12638)
  hydrogen bonds       : bond        0.02937 (  385)
  hydrogen bonds       : angle       3.90747 ( 1101)
  Misc. bond           : bond        0.00012 (    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
  120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.344 
Fit side-chains
REVERT: B  459 GLU cc_start: 0.8212 (pp20) cc_final: 0.7790 (pp20)
REVERT: B  494 PHE cc_start: 0.8076 (m-80) cc_final: 0.7642 (m-80)
REVERT: B  520 ASP cc_start: 0.9036 (t0) cc_final: 0.8829 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 117
  average time/residue: 0.5058
  time to fit residues: 63.7856
Evaluate side-chains
  108 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    0.1980
   chunk 78 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0870
   chunk 36 optimal weight:    0.2980
   chunk 49 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.4960

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.124735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.078979 restraints weight = 15144.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 2.98
r_work: 0.2810 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9336  Z= 0.099
  Angle     :  0.504   6.836  12638  Z= 0.253
  Chirality :  0.044   0.158   1428
  Planarity :  0.003   0.055   1640
  Dihedral  : 10.450 167.285   1370
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.99 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1175
  helix:  1.18 (0.26), residues: 427
  sheet:  1.34 (0.35), residues: 223
  loop : -0.72 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  61 
 TYR   0.020   0.001   TYR B 417 
 PHE   0.010   0.001   PHE B 384 
 TRP   0.005   0.001   TRP A 284 
 HIS   0.004   0.000   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9335)
  covalent geometry    : angle       0.50442 (12638)
  hydrogen bonds       : bond        0.03114 (  385)
  hydrogen bonds       : angle       3.87935 ( 1101)
  Misc. bond           : bond        0.00006 (    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
  123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B  459 GLU cc_start: 0.8195 (pp20) cc_final: 0.7751 (pp20)
REVERT: B  494 PHE cc_start: 0.8027 (m-80) cc_final: 0.7542 (m-80)
REVERT: F   59 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.6309 (m-70)
  outliers start: 16
  outliers final: 10
  residues processed: 122
  average time/residue: 0.5303
  time to fit residues: 69.7173
Evaluate side-chains
  112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  446 ASP
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain F residue   59 HIS
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 116 optimal weight:    0.0470
   overall best weight:    1.5082

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.121994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.076050 restraints weight = 15211.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 2.92
r_work: 0.2776 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9336  Z= 0.203
  Angle     :  0.572   6.986  12638  Z= 0.293
  Chirality :  0.047   0.222   1428
  Planarity :  0.004   0.053   1640
  Dihedral  : 10.512 164.537   1370
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.59 %
    Favored  : 83.55 %
  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:  1.04 (0.26), residues: 425
  sheet:  0.98 (0.35), residues: 234
  loop : -0.75 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  61 
 TYR   0.015   0.001   TYR B 417 
 PHE   0.015   0.001   PHE F 122 
 TRP   0.006   0.001   TRP A 394 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9335)
  covalent geometry    : angle       0.57199 (12638)
  hydrogen bonds       : bond        0.04551 (  385)
  hydrogen bonds       : angle       4.12604 ( 1101)
  Misc. bond           : bond        0.00042 (    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
  132 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.412 
Fit side-chains
REVERT: B  459 GLU cc_start: 0.8314 (pp20) cc_final: 0.7796 (pp20)
REVERT: B  494 PHE cc_start: 0.8110 (m-80) cc_final: 0.7569 (m-80)
REVERT: F   59 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.6287 (m-70)
  outliers start: 28
  outliers final: 18
  residues processed: 125
  average time/residue: 0.5150
  time to fit residues: 69.1903
Evaluate side-chains
  117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  446 ASP
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain F residue   59 HIS
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  278 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 110 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.7186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.121535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.075743 restraints weight = 15192.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.91
r_work: 0.2768 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9336  Z= 0.225
  Angle     :  0.589   7.269  12638  Z= 0.302
  Chirality :  0.048   0.262   1428
  Planarity :  0.004   0.054   1640
  Dihedral  : 10.501 162.341   1370
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.20 %
    Favored  : 83.45 %
  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 (0.25), residues: 1175
  helix:  0.94 (0.26), residues: 423
  sheet:  0.88 (0.34), residues: 234
  loop : -0.84 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  61 
 TYR   0.015   0.001   TYR F 176 
 PHE   0.015   0.002   PHE F 122 
 TRP   0.007   0.001   TRP A 394 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 9335)
  covalent geometry    : angle       0.58852 (12638)
  hydrogen bonds       : bond        0.04661 (  385)
  hydrogen bonds       : angle       4.19108 ( 1101)
  Misc. bond           : bond        0.00047 (    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: 23
    poor density    : 103
  time to evaluate  : 0.338 
Fit side-chains
REVERT: B  459 GLU cc_start: 0.8310 (pp20) cc_final: 0.7742 (pp20)
REVERT: F   59 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6107 (m-70)
  outliers start: 23
  outliers final: 19
  residues processed: 122
  average time/residue: 0.5200
  time to fit residues: 68.2294
Evaluate side-chains
  119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain F residue   59 HIS
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  147 GLN
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  291 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0370
   chunk 82 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.123742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.078209 restraints weight = 15163.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.91
r_work: 0.2817 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9336  Z= 0.120
  Angle     :  0.555   8.723  12638  Z= 0.278
  Chirality :  0.045   0.185   1428
  Planarity :  0.003   0.056   1640
  Dihedral  : 10.279 160.199   1370
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.32 %
    Favored  : 82.94 %
  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:  0.41 (0.25), residues: 1175
  helix:  1.14 (0.26), residues: 424
  sheet:  0.99 (0.34), residues: 232
  loop : -0.76 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  61 
 TYR   0.020   0.001   TYR B 417 
 PHE   0.011   0.001   PHE B 384 
 TRP   0.006   0.001   TRP A 284 
 HIS   0.004   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9335)
  covalent geometry    : angle       0.55481 (12638)
  hydrogen bonds       : bond        0.03410 (  385)
  hydrogen bonds       : angle       3.98367 ( 1101)
  Misc. bond           : bond        0.00017 (    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
  118 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.338 
Fit side-chains
REVERT: B  459 GLU cc_start: 0.8225 (pp20) cc_final: 0.7764 (pp20)
REVERT: B  494 PHE cc_start: 0.8102 (m-80) cc_final: 0.7596 (m-80)
REVERT: F   59 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.6262 (m-70)
  outliers start: 17
  outliers final: 15
  residues processed: 117
  average time/residue: 0.5322
  time to fit residues: 66.9846
Evaluate side-chains
  117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain F residue   59 HIS
Chi-restraints excluded: chain F residue  278 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:   20.0000
   chunk 60 optimal weight:    0.0270
   chunk 12 optimal weight:    0.0030
   chunk 22 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   overall best weight:    1.0054

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.123075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.077506 restraints weight = 15191.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 2.92
r_work: 0.2803 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9336  Z= 0.148
  Angle     :  0.560   8.676  12638  Z= 0.285
  Chirality :  0.045   0.171   1428
  Planarity :  0.004   0.055   1640
  Dihedral  : 10.226 157.850   1370
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.32 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.25), residues: 1175
  helix:  1.11 (0.26), residues: 424
  sheet:  0.98 (0.34), residues: 232
  loop : -0.80 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  61 
 TYR   0.021   0.001   TYR B 417 
 PHE   0.011   0.001   PHE B 384 
 TRP   0.006   0.001   TRP A 284 
 HIS   0.007   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9335)
  covalent geometry    : angle       0.55957 (12638)
  hydrogen bonds       : bond        0.03845 (  385)
  hydrogen bonds       : angle       4.02855 ( 1101)
  Misc. bond           : bond        0.00025 (    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
  120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  726 GLU cc_start: 0.8622 (tp30) cc_final: 0.8419 (tp30)
REVERT: B  459 GLU cc_start: 0.8235 (pp20) cc_final: 0.7763 (pp20)
REVERT: B  494 PHE cc_start: 0.8067 (m-80) cc_final: 0.7577 (m-80)
REVERT: F   59 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.6255 (m-70)
  outliers start: 18
  outliers final: 16
  residues processed: 118
  average time/residue: 0.5313
  time to fit residues: 67.5190
Evaluate side-chains
  117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  499 ARG
Chi-restraints excluded: chain F residue   59 HIS
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  291 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0000
   chunk 51 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.9788

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.123347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.077856 restraints weight = 14980.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.90
r_work: 0.2804 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9336  Z= 0.145
  Angle     :  0.556   8.170  12638  Z= 0.283
  Chirality :  0.045   0.176   1428
  Planarity :  0.004   0.056   1640
  Dihedral  : 10.145 155.506   1370
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.22 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.25), residues: 1175
  helix:  1.17 (0.26), residues: 421
  sheet:  0.96 (0.34), residues: 232
  loop : -0.82 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  61 
 TYR   0.015   0.001   TYR F 176 
 PHE   0.011   0.001   PHE B 384 
 TRP   0.006   0.001   TRP A 284 
 HIS   0.006   0.001   HIS F 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9335)
  covalent geometry    : angle       0.55554 (12638)
  hydrogen bonds       : bond        0.03794 (  385)
  hydrogen bonds       : angle       4.03412 ( 1101)
  Misc. bond           : bond        0.00029 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2903.85 seconds
wall clock time: 50 minutes 19.53 seconds (3019.53 seconds total)