Starting phenix.real_space_refine
on Sun May  3 03:44:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rye_54377/05_2026/9rye_54377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rye_54377/05_2026/9rye_54377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rye_54377/05_2026/9rye_54377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rye_54377/05_2026/9rye_54377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rye_54377/05_2026/9rye_54377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rye_54377/05_2026/9rye_54377.cif"
  }
  resolution = 3.02
  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=  -0.002 sd=   0.035
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      25      5.16       5
     C    6558      2.51       5
     N    1792      2.21       5
     O    1787      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 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: 10168
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4701
          Classifications: {'peptide': 587}
          Link IDs: {'PTRANS': 24, 'TRANS': 562}
    Chain: "B"
      Number of atoms: 4508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4508
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 18, 'TRANS': 552}
    Chain: "C"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 897
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.67, per 1000 atoms: 0.26
  Number of scatterers: 10168
  At special positions: 0
  Unit cell: (71.25, 91.2, 160.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P       6     15.00
     O    1787      8.00
     N    1792      7.00
     C    6558      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 440.3 milliseconds
  

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2340

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 7 sheets defined
      66.5% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 23
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.600A  pdb=" N   LEU A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 4.104A  pdb=" N   PHE A  50 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 120
      removed outlier: 3.584A  pdb=" N   GLU A  68 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ARG A  69 " --> pdb=" O   PRO A  65 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   PHE A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   LEU A  74 " --> pdb=" O   PHE A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 128
      removed outlier: 3.861A  pdb=" N   TYR A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 150
      removed outlier: 3.977A  pdb=" N   ASP A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   VAL A 141 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 173
      removed outlier: 4.041A  pdb=" N   PHE A 160 " --> pdb=" O   ILE A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
    Processing helix  chain 'A' and resid 183 through 222
      removed outlier: 4.131A  pdb=" N   SER A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 231 through 286
      removed outlier: 3.649A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TRP A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LEU A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A 260 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   PHE A 261 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.935A  pdb=" N   GLY A 281 " --> pdb=" O   TYR A 277 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU A 282 " --> pdb=" O   TYR A 278 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 313
      Proline residue:  A 306  - end of helix
    Processing helix  chain 'A' and resid 313 through 333
    Processing helix  chain 'A' and resid 399 through 408
      removed outlier: 3.733A  pdb=" N   VAL A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 435
    Processing helix  chain 'A' and resid 450 through 455
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.565A  pdb=" N   VAL A 466 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 481
    Processing helix  chain 'A' and resid 484 through 487
    Processing helix  chain 'A' and resid 491 through 495
    Processing helix  chain 'A' and resid 498 through 512
    Processing helix  chain 'A' and resid 529 through 545
      removed outlier: 3.948A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 545 " --> pdb=" O   TYR A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
      removed outlier: 4.035A  pdb=" N   ARG A 560 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 586
    Processing helix  chain 'A' and resid 587 through 597
    Processing helix  chain 'B' and resid 6 through 19
      removed outlier: 3.726A  pdb=" N   LEU B  10 " --> pdb=" O   ALA B   6 " (cutoff:3.500A)
      Proline residue:  B  15  - end of helix
      removed outlier: 3.645A  pdb=" N   ARG B  19 " --> pdb=" O   PRO B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 39
    Processing helix  chain 'B' and resid 40 through 53
    Processing helix  chain 'B' and resid 59 through 103
      removed outlier: 3.663A  pdb=" N   LEU B  63 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 3.741A  pdb=" N   TYR B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 134
      removed outlier: 3.875A  pdb=" N   ASP B 125 " --> pdb=" O   ARG B 121 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   LEU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL B 129 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 158
      removed outlier: 3.518A  pdb=" N   VAL B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 167
    Processing helix  chain 'B' and resid 168 through 207
      removed outlier: 3.666A  pdb=" N   ILE B 172 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA B 175 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG B 177 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   PHE B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLU B 192 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 215
    Processing helix  chain 'B' and resid 216 through 243
      removed outlier: 3.525A  pdb=" N   LEU B 227 " --> pdb=" O   TRP B 223 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 270
      removed outlier: 3.895A  pdb=" N   ALA B 247 " --> pdb=" O   GLY B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 317
      removed outlier: 4.437A  pdb=" N   TRP B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      Proline residue:  B 291  - end of helix
      removed outlier: 4.305A  pdb=" N   GLY B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
    Processing helix  chain 'B' and resid 376 through 384
      removed outlier: 4.124A  pdb=" N   VAL B 384 " --> pdb=" O   LEU B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 413
    Processing helix  chain 'B' and resid 427 through 433
    Processing helix  chain 'B' and resid 440 through 451
    Processing helix  chain 'B' and resid 453 through 459
    Processing helix  chain 'B' and resid 462 through 466
    Processing helix  chain 'B' and resid 469 through 473
    Processing helix  chain 'B' and resid 476 through 490
    Processing helix  chain 'B' and resid 506 through 519
      removed outlier: 4.295A  pdb=" N   THR B 519 " --> pdb=" O   GLN B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 537
    Processing helix  chain 'B' and resid 555 through 561
    Processing helix  chain 'B' and resid 563 through 575
      removed outlier: 3.938A  pdb=" N   ALA B 567 " --> pdb=" O   GLY B 563 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.791A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379
      removed outlier: 6.014A  pdb=" N   LYS A 377 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   LEU A 360 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 358 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   PHE A 355 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   PHE A 418 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASP A 357 " --> pdb=" O   CYS A 416 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   CYS A 416 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ARG A 414 " --> pdb=" O   TRP A 359 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 6.487A  pdb=" N   LEU A 519 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ILE A 552 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU A 521 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   LEU A 566 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ALA A 390 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL A 392 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU A 575 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 448 through 449
    Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 361
      removed outlier: 6.171A  pdb=" N   LEU B 353 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   LYS B 347 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ARG B 355 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   GLY B 345 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   LEU B 357 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B 343 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   GLU B 392 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   HIS B 400 " --> pdb=" O   VAL B 397 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.869A  pdb=" N   THR B 366 " --> pdb=" O   TRP B 541 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE B 543 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLY B 368 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   LEU B 545 " --> pdb=" O   GLY B 368 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   THR B 370 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ILE B 542 " --> pdb=" O   GLU B 553 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLU B 553 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL B 544 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12
      removed outlier: 5.866A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    657 hydrogen bonds defined for protein.
    1905 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3338
        1.34 -     1.46: 2075
        1.46 -     1.58: 4917
        1.58 -     1.69: 8
        1.69 -     1.81: 45
  Bond restraints: 10383
  Sorted by residual:
  bond pdb=" C1' ATP B 601 "
       pdb=" O4' ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.416  1.398  0.018 1.30e-02 5.92e+03 1.83e+00
  bond pdb=" CG  ARG A 208 "
       pdb=" CD  ARG A 208 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.56e+00
  bond pdb=" C1' ATP A 701 "
       pdb=" O4' ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.416  1.402  0.014 1.30e-02 5.92e+03 1.24e+00
  bond pdb=" C4' ATP A 701 "
       pdb=" O4' ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.444  1.432  0.012 1.10e-02 8.26e+03 1.23e+00
  bond pdb=" CG1 ILE A 254 "
       pdb=" CD1 ILE A 254 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.11e+00
  ... (remaining 10378 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 13498
        1.31 -     2.63: 469
        2.63 -     3.94: 101
        3.94 -     5.25: 11
        5.25 -     6.57: 10
  Bond angle restraints: 14089
  Sorted by residual:
  angle pdb=" N   SER A 514 "
        pdb=" CA  SER A 514 "
        pdb=" C   SER A 514 "
      ideal   model   delta    sigma   weight residual
     108.13  110.96   -2.83 9.00e-01 1.23e+00 9.87e+00
  angle pdb=" C3' ATP B 601 "
        pdb=" C4' ATP B 601 "
        pdb=" C5' ATP B 601 "
      ideal   model   delta    sigma   weight residual
     115.19  110.50    4.69 1.76e+00 3.23e-01 7.11e+00
  angle pdb=" N   GLY A 396 "
        pdb=" CA  GLY A 396 "
        pdb=" C   GLY A 396 "
      ideal   model   delta    sigma   weight residual
     113.18  107.04    6.14 2.37e+00 1.78e-01 6.71e+00
  angle pdb=" C4' ATP A 701 "
        pdb=" C3' ATP A 701 "
        pdb=" O3' ATP A 701 "
      ideal   model   delta    sigma   weight residual
     111.06  104.86    6.20 2.50e+00 1.60e-01 6.15e+00
  angle pdb=" C2' ATP A 701 "
        pdb=" C3' ATP A 701 "
        pdb=" O3' ATP A 701 "
      ideal   model   delta    sigma   weight residual
     111.83  105.50    6.33 2.67e+00 1.40e-01 5.62e+00
  ... (remaining 14084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 5672
       17.73 -    35.47: 445
       35.47 -    53.20: 57
       53.20 -    70.94: 13
       70.94 -    88.67: 11
  Dihedral angle restraints: 6198
    sinusoidal: 2542
      harmonic: 3656
  Sorted by residual:
  dihedral pdb=" CA  LEU C 103 "
           pdb=" C   LEU C 103 "
           pdb=" N   LEU C 104 "
           pdb=" CA  LEU C 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.51  -19.49     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  ARG B 386 "
           pdb=" C   ARG B 386 "
           pdb=" N   LEU B 387 "
           pdb=" CA  LEU B 387 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  ARG C  19 "
           pdb=" C   ARG C  19 "
           pdb=" N   LEU C  20 "
           pdb=" CA  LEU C  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.37   16.63     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 6195 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1398
       0.058 -    0.115: 179
       0.115 -    0.173: 22
       0.173 -    0.230: 0
       0.230 -    0.288: 6
  Chirality restraints: 1605
  Sorted by residual:
  chirality pdb=" C3' ATP A 701 "
            pdb=" C2' ATP A 701 "
            pdb=" C4' ATP A 701 "
            pdb=" O3' ATP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.92    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" C2' ATP B 601 "
            pdb=" C1' ATP B 601 "
            pdb=" C3' ATP B 601 "
            pdb=" O2' ATP B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" C3' ATP B 601 "
            pdb=" C2' ATP B 601 "
            pdb=" C4' ATP B 601 "
            pdb=" O3' ATP B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 1602 not shown)

  Planarity restraints: 1780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 355 "    0.216 9.50e-02 1.11e+02   9.70e-02 6.54e+00
        pdb=" NE  ARG B 355 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 355 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 355 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 355 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 493 "   -0.147 9.50e-02 1.11e+02   6.59e-02 2.70e+00
        pdb=" NE  ARG A 493 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 493 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 493 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 493 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 245 "   -0.007 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" CG  ASP A 245 "    0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 245 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 245 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1777 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2928
        2.82 -     3.34: 10330
        3.34 -     3.86: 16918
        3.86 -     4.38: 20363
        4.38 -     4.90: 34650
  Nonbonded interactions: 85189
  Sorted by model distance:
  nonbonded pdb=" O2' ATP B 601 "
            pdb=" O3' ATP B 601 "
     model   vdw
     2.301 2.432
  nonbonded pdb=" O2' ATP A 701 "
            pdb=" O3' ATP A 701 "
     model   vdw
     2.312 2.432
  nonbonded pdb=" O   ASP A 373 "
            pdb=" OD1 ASP A 373 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   ASP A 411 "
            pdb=" OD1 ASP A 411 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O   THR A 525 "
            pdb=" OG1 THR A 525 "
     model   vdw
     2.414 3.040
  ... (remaining 85184 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:             2.610
  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:                    0.040
  Process input model:                     11.930
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
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      :  0.004   0.041  10385  Z= 0.183
  Angle     :  0.611   6.568  14093  Z= 0.332
  Chirality :  0.043   0.288   1605
  Planarity :  0.005   0.097   1780
  Dihedral  : 12.877  88.671   3852
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  0.21 (0.23), residues: 1273
  helix:  1.00 (0.18), residues: 783
  sheet: -1.04 (0.46), residues: 114
  loop : -1.20 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 355 
 TYR   0.012   0.001   TYR A 427 
 PHE   0.019   0.001   PHE A 296 
 TRP   0.018   0.002   TRP B 223 
 HIS   0.005   0.001   HIS B 556 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10383)
  covalent geometry    : angle       0.61079 (14089)
  SS BOND              : bond        0.00319 (    2)
  SS BOND              : angle       1.02980 (    4)
  hydrogen bonds       : bond        0.11517 (  657)
  hydrogen bonds       : angle       5.36806 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ARG cc_start: 0.6782 (ttp-170) cc_final: 0.5988 (ttm170)
REVERT: A  218 GLU cc_start: 0.7651 (tp30) cc_final: 0.7342 (tt0)
REVERT: A  389 VAL cc_start: 0.8956 (m) cc_final: 0.8698 (t)
REVERT: A  517 ILE cc_start: 0.6119 (tt) cc_final: 0.5862 (tt)
REVERT: A  569 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7973 (mtp-110)
REVERT: B  185 ARG cc_start: 0.7117 (ttp-170) cc_final: 0.6769 (ttp80)
REVERT: B  218 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7692 (mtm-85)
REVERT: B  223 TRP cc_start: 0.7032 (t-100) cc_final: 0.6789 (t60)
REVERT: B  323 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7174 (mtp-110)
REVERT: B  412 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8148 (mtpt)
REVERT: B  430 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7233 (mt-10)
REVERT: B  555 THR cc_start: 0.8734 (m) cc_final: 0.8414 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.1489
  time to fit residues: 38.0000
Evaluate side-chains
  159 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.0770
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    0.0870
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
A 217 GLN
A 318 GLN
A 429 GLN
B 123 ASN
B 287 GLN
** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.158944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.124577 restraints weight = 11938.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.21
r_work: 0.3285 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10385  Z= 0.127
  Angle     :  0.544   6.625  14093  Z= 0.276
  Chirality :  0.039   0.154   1605
  Planarity :  0.004   0.044   1780
  Dihedral  :  6.017  74.707   1501
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  6.02 %
    Favored  : 92.84 %
  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:  0.68 (0.23), residues: 1273
  helix:  1.30 (0.18), residues: 795
  sheet: -0.89 (0.45), residues: 118
  loop : -0.88 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 482 
 TYR   0.011   0.001   TYR A 427 
 PHE   0.021   0.001   PHE B  38 
 TRP   0.012   0.001   TRP B 223 
 HIS   0.003   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10383)
  covalent geometry    : angle       0.54383 (14089)
  SS BOND              : bond        0.00155 (    2)
  SS BOND              : angle       0.69364 (    4)
  hydrogen bonds       : bond        0.04141 (  657)
  hydrogen bonds       : angle       4.43092 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8854 (m110) cc_final: 0.8559 (m110)
REVERT: A  158 ASP cc_start: 0.7796 (m-30) cc_final: 0.7564 (m-30)
REVERT: A  195 ARG cc_start: 0.7137 (ttp-170) cc_final: 0.6344 (ttm170)
REVERT: A  204 GLU cc_start: 0.8042 (tp30) cc_final: 0.7781 (tt0)
REVERT: A  237 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7441 (mt-10)
REVERT: A  332 ASP cc_start: 0.7273 (m-30) cc_final: 0.7073 (m-30)
REVERT: A  336 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7751 (mt-10)
REVERT: A  517 ILE cc_start: 0.6182 (tt) cc_final: 0.5844 (tt)
REVERT: A  569 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8088 (mtp-110)
REVERT: B   89 GLN cc_start: 0.8421 (mt0) cc_final: 0.7921 (mm-40)
REVERT: B  185 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7043 (ttp80)
REVERT: B  218 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7792 (mtm-85)
REVERT: B  219 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7930 (ttm110)
REVERT: B  240 ARG cc_start: 0.7294 (ptp90) cc_final: 0.7047 (ptp90)
REVERT: B  336 SER cc_start: 0.8740 (m) cc_final: 0.8368 (t)
REVERT: B  412 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8365 (mtpt)
REVERT: B  430 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7580 (mt-10)
REVERT: B  555 THR cc_start: 0.8978 (m) cc_final: 0.8605 (p)
  outliers start: 12
  outliers final: 3
  residues processed: 176
  average time/residue: 0.1393
  time to fit residues: 32.4260
Evaluate side-chains
  153 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain C residue    5 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   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 213 ASN
** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.121791 restraints weight = 11995.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.21
r_work: 0.3244 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10385  Z= 0.147
  Angle     :  0.538   9.316  14093  Z= 0.272
  Chirality :  0.040   0.139   1605
  Planarity :  0.004   0.045   1780
  Dihedral  :  6.045  74.432   1501
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  8.60 %
    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:  0.86 (0.23), residues: 1273
  helix:  1.48 (0.18), residues: 795
  sheet: -0.79 (0.44), residues: 120
  loop : -0.92 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 433 
 TYR   0.010   0.001   TYR C  95 
 PHE   0.020   0.001   PHE B  38 
 TRP   0.011   0.001   TRP B 541 
 HIS   0.004   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10383)
  covalent geometry    : angle       0.53787 (14089)
  SS BOND              : bond        0.00196 (    2)
  SS BOND              : angle       0.63433 (    4)
  hydrogen bonds       : bond        0.03964 (  657)
  hydrogen bonds       : angle       4.19161 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8860 (m110) cc_final: 0.8591 (m110)
REVERT: A  158 ASP cc_start: 0.7762 (m-30) cc_final: 0.7425 (m-30)
REVERT: A  195 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6352 (ttm170)
REVERT: A  321 MET cc_start: 0.8005 (tpp) cc_final: 0.7734 (tpp)
REVERT: A  332 ASP cc_start: 0.7376 (m-30) cc_final: 0.7120 (m-30)
REVERT: A  517 ILE cc_start: 0.6230 (tt) cc_final: 0.5849 (tt)
REVERT: B   45 LEU cc_start: 0.8078 (tp) cc_final: 0.7874 (tt)
REVERT: B  185 ARG cc_start: 0.7331 (ttp-170) cc_final: 0.7077 (ttp80)
REVERT: B  192 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7864 (mt-10)
REVERT: B  218 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7947 (mtm-85)
REVERT: B  219 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7846 (ttm110)
REVERT: B  240 ARG cc_start: 0.7382 (ptp90) cc_final: 0.7068 (ptp90)
REVERT: B  336 SER cc_start: 0.8737 (m) cc_final: 0.8386 (t)
REVERT: B  412 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8415 (mtpt)
REVERT: B  430 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7589 (mt-10)
REVERT: B  553 GLU cc_start: 0.9002 (pt0) cc_final: 0.8577 (pt0)
REVERT: B  555 THR cc_start: 0.8919 (m) cc_final: 0.8571 (p)
REVERT: B  569 MET cc_start: 0.6740 (mtp) cc_final: 0.6356 (ptp)
REVERT: C   82 GLN cc_start: 0.7906 (mm110) cc_final: 0.7694 (mm-40)
  outliers start: 18
  outliers final: 12
  residues processed: 165
  average time/residue: 0.1598
  time to fit residues: 33.9291
Evaluate side-chains
  161 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain B residue  546 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 89 optimal weight:    0.0980
   chunk 34 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
A 302 GLN
A 537 GLN
B  89 GLN
B 303 GLN
C  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.158606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123820 restraints weight = 12064.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.22
r_work: 0.3273 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10385  Z= 0.115
  Angle     :  0.504   9.649  14093  Z= 0.254
  Chirality :  0.038   0.146   1605
  Planarity :  0.004   0.035   1780
  Dihedral  :  5.878  78.767   1501
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.51 %
    Favored  : 88.16 %
  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:  1.15 (0.24), residues: 1273
  helix:  1.70 (0.18), residues: 796
  sheet: -0.65 (0.44), residues: 118
  loop : -0.82 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 304 
 TYR   0.012   0.001   TYR B 284 
 PHE   0.018   0.001   PHE A 296 
 TRP   0.009   0.001   TRP B 541 
 HIS   0.003   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10383)
  covalent geometry    : angle       0.50355 (14089)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       0.43720 (    4)
  hydrogen bonds       : bond        0.03611 (  657)
  hydrogen bonds       : angle       4.03384 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8834 (m110) cc_final: 0.8630 (m110)
REVERT: A  158 ASP cc_start: 0.7786 (m-30) cc_final: 0.7414 (m-30)
REVERT: A  195 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6435 (ttm170)
REVERT: A  380 SER cc_start: 0.8531 (t) cc_final: 0.8272 (p)
REVERT: A  517 ILE cc_start: 0.5946 (tt) cc_final: 0.5576 (tt)
REVERT: B   45 LEU cc_start: 0.8052 (tp) cc_final: 0.7846 (tt)
REVERT: B  173 PHE cc_start: 0.6691 (t80) cc_final: 0.6375 (m-80)
REVERT: B  185 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7076 (ttp80)
REVERT: B  192 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7877 (mt-10)
REVERT: B  218 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7941 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7754 (ttm-80)
REVERT: B  336 SER cc_start: 0.8638 (m) cc_final: 0.8316 (t)
REVERT: B  430 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7565 (mt-10)
REVERT: B  555 THR cc_start: 0.8834 (m) cc_final: 0.8544 (p)
REVERT: B  569 MET cc_start: 0.6642 (mtp) cc_final: 0.6218 (ptp)
REVERT: C   18 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7004 (tt)
REVERT: C   65 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8237 (ttmt)
REVERT: C   82 GLN cc_start: 0.7984 (mm110) cc_final: 0.7731 (mm-40)
  outliers start: 14
  outliers final: 8
  residues processed: 171
  average time/residue: 0.1311
  time to fit residues: 29.6784
Evaluate side-chains
  158 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   18 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 121 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 102 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 122 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
A 537 GLN
B 400 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.156452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.121493 restraints weight = 11942.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.19
r_work: 0.3229 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10385  Z= 0.144
  Angle     :  0.524   9.256  14093  Z= 0.262
  Chirality :  0.039   0.149   1605
  Planarity :  0.004   0.038   1780
  Dihedral  :  5.961  77.284   1501
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.46 %
    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:  1.15 (0.24), residues: 1273
  helix:  1.67 (0.18), residues: 798
  sheet: -0.61 (0.44), residues: 118
  loop : -0.77 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 304 
 TYR   0.017   0.001   TYR B 284 
 PHE   0.015   0.001   PHE B  38 
 TRP   0.010   0.001   TRP B 541 
 HIS   0.004   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10383)
  covalent geometry    : angle       0.52359 (14089)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.53303 (    4)
  hydrogen bonds       : bond        0.03796 (  657)
  hydrogen bonds       : angle       4.03448 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLN cc_start: 0.8157 (mt0) cc_final: 0.7927 (pt0)
REVERT: A  128 ASN cc_start: 0.8839 (m110) cc_final: 0.8611 (m110)
REVERT: A  158 ASP cc_start: 0.7752 (m-30) cc_final: 0.7370 (m-30)
REVERT: A  195 ARG cc_start: 0.7160 (ttp-170) cc_final: 0.6404 (ttm170)
REVERT: A  252 GLU cc_start: 0.7701 (tp30) cc_final: 0.7158 (mt-10)
REVERT: A  332 ASP cc_start: 0.7613 (m-30) cc_final: 0.6849 (p0)
REVERT: A  380 SER cc_start: 0.8573 (t) cc_final: 0.8294 (p)
REVERT: A  517 ILE cc_start: 0.6009 (tt) cc_final: 0.5713 (tt)
REVERT: B   45 LEU cc_start: 0.8013 (tp) cc_final: 0.7805 (tt)
REVERT: B  173 PHE cc_start: 0.6593 (t80) cc_final: 0.6279 (m-80)
REVERT: B  218 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7905 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.7905 (ttm110)
REVERT: B  336 SER cc_start: 0.8477 (m) cc_final: 0.8272 (t)
REVERT: B  430 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7608 (mt-10)
REVERT: B  555 THR cc_start: 0.8828 (m) cc_final: 0.8530 (p)
REVERT: B  569 MET cc_start: 0.6700 (mtp) cc_final: 0.6362 (ptp)
REVERT: C   18 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7139 (tt)
REVERT: C   30 ASP cc_start: 0.7824 (t0) cc_final: 0.7541 (p0)
REVERT: C   82 GLN cc_start: 0.7973 (mm110) cc_final: 0.7675 (mm110)
  outliers start: 18
  outliers final: 9
  residues processed: 164
  average time/residue: 0.1282
  time to fit residues: 28.0666
Evaluate side-chains
  159 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain B residue  546 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   18 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
A 537 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.120466 restraints weight = 12042.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.21
r_work: 0.3218 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10385  Z= 0.147
  Angle     :  0.530   8.484  14093  Z= 0.264
  Chirality :  0.040   0.150   1605
  Planarity :  0.004   0.039   1780
  Dihedral  :  5.992  77.724   1501
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.70 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.23), residues: 1273
  helix:  1.69 (0.18), residues: 790
  sheet: -0.49 (0.43), residues: 122
  loop : -0.76 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 107 
 TYR   0.019   0.001   TYR B 284 
 PHE   0.014   0.001   PHE B  38 
 TRP   0.011   0.001   TRP B 541 
 HIS   0.005   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10383)
  covalent geometry    : angle       0.53001 (14089)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       0.54169 (    4)
  hydrogen bonds       : bond        0.03791 (  657)
  hydrogen bonds       : angle       4.04107 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8805 (m110) cc_final: 0.8552 (m110)
REVERT: A  158 ASP cc_start: 0.7719 (m-30) cc_final: 0.7295 (m-30)
REVERT: A  195 ARG cc_start: 0.7033 (ttp-170) cc_final: 0.6236 (ttm170)
REVERT: A  252 GLU cc_start: 0.7863 (tp30) cc_final: 0.7194 (mt-10)
REVERT: A  332 ASP cc_start: 0.7697 (m-30) cc_final: 0.6931 (p0)
REVERT: A  380 SER cc_start: 0.8599 (t) cc_final: 0.8296 (p)
REVERT: A  517 ILE cc_start: 0.5991 (tt) cc_final: 0.5592 (tt)
REVERT: B   11 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8067 (ttp-170)
REVERT: B   45 LEU cc_start: 0.7925 (tp) cc_final: 0.7722 (tt)
REVERT: B   46 ARG cc_start: 0.6959 (tmm-80) cc_final: 0.6665 (ttt-90)
REVERT: B  218 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7902 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7702 (ttm-80)
REVERT: B  336 SER cc_start: 0.8502 (m) cc_final: 0.8254 (t)
REVERT: B  430 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7559 (mt-10)
REVERT: B  555 THR cc_start: 0.8808 (m) cc_final: 0.8498 (p)
REVERT: B  569 MET cc_start: 0.6634 (mtp) cc_final: 0.6207 (ptp)
REVERT: C   82 GLN cc_start: 0.8004 (mm110) cc_final: 0.7643 (mm110)
  outliers start: 20
  outliers final: 16
  residues processed: 159
  average time/residue: 0.1364
  time to fit residues: 28.4916
Evaluate side-chains
  164 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain B residue  546 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0070
   chunk 115 optimal weight:   10.0000
   chunk 118 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
A 213 ASN
A 537 GLN
C  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.156404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.121654 restraints weight = 11946.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.20
r_work: 0.3236 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10385  Z= 0.127
  Angle     :  0.512   8.167  14093  Z= 0.255
  Chirality :  0.039   0.160   1605
  Planarity :  0.004   0.036   1780
  Dihedral  :  5.918  79.254   1501
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.47 %
    Favored  : 84.91 %
  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:  1.29 (0.23), residues: 1273
  helix:  1.77 (0.18), residues: 790
  sheet: -0.37 (0.45), residues: 112
  loop : -0.68 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 107 
 TYR   0.017   0.001   TYR B 284 
 PHE   0.014   0.001   PHE B  38 
 TRP   0.009   0.001   TRP B 541 
 HIS   0.005   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10383)
  covalent geometry    : angle       0.51240 (14089)
  SS BOND              : bond        0.00177 (    2)
  SS BOND              : angle       0.42325 (    4)
  hydrogen bonds       : bond        0.03663 (  657)
  hydrogen bonds       : angle       3.98643 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8798 (m110) cc_final: 0.8568 (m110)
REVERT: A  158 ASP cc_start: 0.7731 (m-30) cc_final: 0.7327 (m-30)
REVERT: A  195 ARG cc_start: 0.7034 (ttp-170) cc_final: 0.6293 (ttm170)
REVERT: A  213 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8567 (m-40)
REVERT: A  252 GLU cc_start: 0.7931 (tp30) cc_final: 0.7306 (mt-10)
REVERT: A  332 ASP cc_start: 0.7712 (m-30) cc_final: 0.7072 (p0)
REVERT: A  380 SER cc_start: 0.8600 (t) cc_final: 0.8312 (p)
REVERT: A  517 ILE cc_start: 0.5957 (tt) cc_final: 0.5678 (tt)
REVERT: A  569 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7261 (ttm170)
REVERT: B   11 ARG cc_start: 0.8553 (tpp-160) cc_final: 0.8019 (ttp-170)
REVERT: B   46 ARG cc_start: 0.6997 (tmm-80) cc_final: 0.6728 (ttt-90)
REVERT: B  173 PHE cc_start: 0.6635 (t80) cc_final: 0.6327 (m-80)
REVERT: B  218 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7912 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7730 (ttm-80)
REVERT: B  430 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7532 (mt-10)
REVERT: B  555 THR cc_start: 0.8818 (m) cc_final: 0.8523 (p)
REVERT: C   82 GLN cc_start: 0.8070 (mm110) cc_final: 0.7725 (mm110)
  outliers start: 17
  outliers final: 13
  residues processed: 165
  average time/residue: 0.1423
  time to fit residues: 30.8246
Evaluate side-chains
  164 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain B residue  546 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0060
   chunk 66 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0050
   chunk 71 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.5210

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.156978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.122446 restraints weight = 11888.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.15
r_work: 0.3259 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10385  Z= 0.115
  Angle     :  0.510  10.034  14093  Z= 0.253
  Chirality :  0.038   0.166   1605
  Planarity :  0.004   0.033   1780
  Dihedral  :  5.854  81.037   1501
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.75 %
    Favored  : 84.81 %
  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:  1.37 (0.24), residues: 1273
  helix:  1.82 (0.18), residues: 788
  sheet: -0.24 (0.45), residues: 111
  loop : -0.67 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 107 
 TYR   0.013   0.001   TYR B 284 
 PHE   0.014   0.001   PHE B  38 
 TRP   0.009   0.001   TRP B 541 
 HIS   0.004   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10383)
  covalent geometry    : angle       0.50983 (14089)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.44143 (    4)
  hydrogen bonds       : bond        0.03553 (  657)
  hydrogen bonds       : angle       3.94117 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8784 (m110) cc_final: 0.8562 (m110)
REVERT: A  158 ASP cc_start: 0.7738 (m-30) cc_final: 0.7532 (m-30)
REVERT: A  195 ARG cc_start: 0.6991 (ttp-170) cc_final: 0.6247 (ttm170)
REVERT: A  252 GLU cc_start: 0.7895 (tp30) cc_final: 0.7246 (mt-10)
REVERT: A  332 ASP cc_start: 0.7710 (m-30) cc_final: 0.7074 (p0)
REVERT: A  380 SER cc_start: 0.8519 (t) cc_final: 0.8252 (p)
REVERT: A  569 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7230 (ttm170)
REVERT: B   11 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8003 (ttp-170)
REVERT: B  173 PHE cc_start: 0.6592 (t80) cc_final: 0.6272 (m-80)
REVERT: B  218 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7900 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7731 (ttm-80)
REVERT: B  430 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7471 (mt-10)
REVERT: B  555 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8433 (p)
REVERT: C   82 GLN cc_start: 0.8063 (mm110) cc_final: 0.7617 (mm110)
  outliers start: 15
  outliers final: 14
  residues processed: 158
  average time/residue: 0.1397
  time to fit residues: 28.9316
Evaluate side-chains
  163 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain B residue  546 ASP
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 111 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    0.2980
   chunk 101 optimal weight:    0.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.155751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.121261 restraints weight = 11886.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.18
r_work: 0.3251 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10385  Z= 0.129
  Angle     :  0.518   8.423  14093  Z= 0.257
  Chirality :  0.039   0.164   1605
  Planarity :  0.004   0.034   1780
  Dihedral  :  5.874  80.124   1501
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.94 %
    Favored  : 84.24 %
  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:  1.35 (0.24), residues: 1273
  helix:  1.80 (0.18), residues: 788
  sheet: -0.22 (0.45), residues: 110
  loop : -0.66 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 107 
 TYR   0.013   0.001   TYR C  95 
 PHE   0.013   0.001   PHE B  38 
 TRP   0.010   0.001   TRP B 541 
 HIS   0.005   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10383)
  covalent geometry    : angle       0.51755 (14089)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.45154 (    4)
  hydrogen bonds       : bond        0.03629 (  657)
  hydrogen bonds       : angle       3.94780 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8799 (m110) cc_final: 0.8587 (m110)
REVERT: A  158 ASP cc_start: 0.7814 (m-30) cc_final: 0.7609 (m-30)
REVERT: A  195 ARG cc_start: 0.7012 (ttp-170) cc_final: 0.6265 (ttm170)
REVERT: A  252 GLU cc_start: 0.7874 (tp30) cc_final: 0.7251 (mt-10)
REVERT: A  332 ASP cc_start: 0.7731 (m-30) cc_final: 0.7128 (p0)
REVERT: A  380 SER cc_start: 0.8556 (t) cc_final: 0.8271 (p)
REVERT: A  569 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7234 (ttm170)
REVERT: A  575 GLU cc_start: 0.8367 (tt0) cc_final: 0.8106 (mt-10)
REVERT: B   11 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.7986 (ttp-170)
REVERT: B   46 ARG cc_start: 0.7362 (ttt-90) cc_final: 0.7111 (ttp-170)
REVERT: B  218 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7907 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7769 (ttm-80)
REVERT: B  430 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7476 (mt-10)
REVERT: B  512 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7714 (ttm-80)
REVERT: B  555 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8435 (p)
  outliers start: 19
  outliers final: 17
  residues processed: 159
  average time/residue: 0.1307
  time to fit residues: 27.6325
Evaluate side-chains
  168 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain B residue  546 ASP
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0370
   chunk 117 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.156321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.121824 restraints weight = 11813.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.14
r_work: 0.3245 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10385  Z= 0.123
  Angle     :  0.513   8.853  14093  Z= 0.255
  Chirality :  0.039   0.163   1605
  Planarity :  0.004   0.032   1780
  Dihedral  :  5.856  80.627   1501
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.14 %
    Favored  : 84.05 %
  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:  1.35 (0.24), residues: 1273
  helix:  1.82 (0.18), residues: 787
  sheet: -0.46 (0.45), residues: 115
  loop : -0.60 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 107 
 TYR   0.015   0.001   TYR C  95 
 PHE   0.012   0.001   PHE B  38 
 TRP   0.009   0.001   TRP B 541 
 HIS   0.005   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10383)
  covalent geometry    : angle       0.51337 (14089)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.49367 (    4)
  hydrogen bonds       : bond        0.03596 (  657)
  hydrogen bonds       : angle       3.93278 ( 1905)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8793 (m110) cc_final: 0.8574 (m110)
REVERT: A  158 ASP cc_start: 0.7765 (m-30) cc_final: 0.7562 (m-30)
REVERT: A  195 ARG cc_start: 0.6982 (ttp-170) cc_final: 0.6234 (ttm170)
REVERT: A  252 GLU cc_start: 0.7906 (tp30) cc_final: 0.7247 (mt-10)
REVERT: A  332 ASP cc_start: 0.7701 (m-30) cc_final: 0.7125 (p0)
REVERT: A  380 SER cc_start: 0.8550 (t) cc_final: 0.8276 (p)
REVERT: A  569 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7249 (ttm170)
REVERT: A  575 GLU cc_start: 0.8344 (tt0) cc_final: 0.8091 (mt-10)
REVERT: B   11 ARG cc_start: 0.8526 (tpp-160) cc_final: 0.7999 (ttp-170)
REVERT: B   46 ARG cc_start: 0.7378 (ttt-90) cc_final: 0.6717 (tmm-80)
REVERT: B  218 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7925 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7743 (ttm-80)
REVERT: B  430 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7464 (mt-10)
REVERT: B  512 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7791 (ttm-80)
REVERT: B  555 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8457 (p)
REVERT: C   82 GLN cc_start: 0.7944 (tp40) cc_final: 0.7719 (mm110)
  outliers start: 19
  outliers final: 17
  residues processed: 158
  average time/residue: 0.1242
  time to fit residues: 26.0153
Evaluate side-chains
  170 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  416 CYS
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  473 ILE
Chi-restraints excluded: chain B residue  546 ASP
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0000
   chunk 28 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 79 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 102 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.157015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.122246 restraints weight = 11898.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.20
r_work: 0.3261 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10385  Z= 0.113
  Angle     :  0.506   8.692  14093  Z= 0.251
  Chirality :  0.038   0.163   1605
  Planarity :  0.003   0.032   1780
  Dihedral  :  5.805  81.958   1501
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.42 %
    Favored  : 83.86 %
  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:  1.43 (0.24), residues: 1273
  helix:  1.88 (0.18), residues: 787
  sheet: -0.34 (0.46), residues: 113
  loop : -0.60 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 107 
 TYR   0.015   0.001   TYR C  95 
 PHE   0.013   0.001   PHE B  38 
 TRP   0.009   0.001   TRP B 541 
 HIS   0.004   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10383)
  covalent geometry    : angle       0.50566 (14089)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       0.44307 (    4)
  hydrogen bonds       : bond        0.03523 (  657)
  hydrogen bonds       : angle       3.89948 ( 1905)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2912.48 seconds
wall clock time: 50 minutes 30.60 seconds (3030.60 seconds total)