Starting phenix.real_space_refine
on Wed Jan 22 17:09:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yn1_39411/01_2025/8yn1_39411.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yn1_39411/01_2025/8yn1_39411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yn1_39411/01_2025/8yn1_39411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yn1_39411/01_2025/8yn1_39411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yn1_39411/01_2025/8yn1_39411.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yn1_39411/01_2025/8yn1_39411.cif"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8627 atoms to isotropic.
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       5      5.49       5
     S      62      5.16       5
     C    7762      2.51       5
     N    2047      2.21       5
     O    2310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12186
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4720
          Classifications: {'peptide': 580}
          Link IDs: {'PTRANS': 21, 'TRANS': 558}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4149
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 16, 'TRANS': 492}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3251
          Classifications: {'peptide': 406}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 391}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'APR': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 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: 6.82, per 1000 atoms: 0.56
  Number of scatterers: 12186
  At special positions: 0
  Unit cell: (121.55, 110.5, 130.9, 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      62     16.00
     P       5     15.00
     O    2310      8.00
     N    2047      7.00
     C    7762      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.00
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2856

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 9 sheets defined
      56.0% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 8
    Processing helix  chain 'A' and resid 10 through 24
    Processing helix  chain 'A' and resid 87 through 98
      removed outlier: 3.600A  pdb=" N   ASP A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 102
    Processing helix  chain 'A' and resid 103 through 113
      removed outlier: 3.592A  pdb=" N   SER A 113 " --> pdb=" O   MET A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 140
      removed outlier: 3.599A  pdb=" N   LEU A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 149
    Processing helix  chain 'A' and resid 163 through 173
      removed outlier: 3.536A  pdb=" N   SER A 167 " --> pdb=" O   ASP A 163 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLU A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 5.640A  pdb=" N   MET A 193 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 194 " --> pdb=" O   ARG A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 201
      removed outlier: 3.739A  pdb=" N   VAL A 200 " --> pdb=" O   ARG A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 212
      removed outlier: 3.827A  pdb=" N   VAL A 207 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 246
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 4.267A  pdb=" N   LEU A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 297
      removed outlier: 3.926A  pdb=" N   PHE A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
      removed outlier: 3.581A  pdb=" N   SER A 307 " --> pdb=" O   GLN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 317
      removed outlier: 3.946A  pdb=" N   ILE A 314 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 326
      removed outlier: 3.614A  pdb=" N   LEU A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 348
      removed outlier: 4.031A  pdb=" N   THR A 344 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 381
      removed outlier: 3.638A  pdb=" N   GLN A 381 " --> pdb=" O   GLN A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 394
      removed outlier: 3.892A  pdb=" N   LEU A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE A 391 " --> pdb=" O   LYS A 387 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLU A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 402
    Processing helix  chain 'A' and resid 405 through 413
    Processing helix  chain 'A' and resid 415 through 441
    Processing helix  chain 'A' and resid 447 through 450
    Processing helix  chain 'A' and resid 451 through 476
      Proline residue:  A 467  - end of helix
      removed outlier: 3.683A  pdb=" N   HIS A 476 " --> pdb=" O   ASN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 481
    Processing helix  chain 'A' and resid 484 through 489
      removed outlier: 3.659A  pdb=" N   ARG A 488 " --> pdb=" O   PRO A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 507
      removed outlier: 3.744A  pdb=" N   ILE A 495 " --> pdb=" O   PRO A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 556
      removed outlier: 3.706A  pdb=" N   GLU A 551 " --> pdb=" O   CYS A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 3.724A  pdb=" N   VAL A 563 " --> pdb=" O   PRO A 559 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   VAL A 565 " --> pdb=" O   GLU A 561 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   ARG A 566 " --> pdb=" O   GLU A 562 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   GLY A 575 " --> pdb=" O   GLU A 571 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   GLU A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 600
    Processing helix  chain 'A' and resid 603 through 608
    Processing helix  chain 'B' and resid 4 through 20
      removed outlier: 3.637A  pdb=" N   GLY B  20 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 34
      removed outlier: 4.222A  pdb=" N   SER B  24 " --> pdb=" O   GLY B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 136
      removed outlier: 5.119A  pdb=" N   THR B 121 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   SER B 122 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   TYR B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER B 136 " --> pdb=" O   GLN B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 160
      removed outlier: 3.531A  pdb=" N   SER B 150 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 189
    Processing helix  chain 'B' and resid 192 through 196
    Processing helix  chain 'B' and resid 232 through 241
    Processing helix  chain 'B' and resid 250 through 262
      removed outlier: 3.742A  pdb=" N   VAL B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 317
      removed outlier: 3.874A  pdb=" N   MET B 293 " --> pdb=" O   ARG B 289 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE B 294 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   ASN B 298 " --> pdb=" O   PHE B 294 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ASP B 299 " --> pdb=" O   LYS B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 331
    Processing helix  chain 'B' and resid 334 through 360
      removed outlier: 3.773A  pdb=" N   ILE B 338 " --> pdb=" O   LYS B 334 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LYS B 345 " --> pdb=" O   LYS B 341 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   SER B 346 " --> pdb=" O   ASN B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 396
      Proline residue:  B 387  - end of helix
    Processing helix  chain 'B' and resid 400 through 405
    Processing helix  chain 'B' and resid 407 through 422
      removed outlier: 3.629A  pdb=" N   VAL B 411 " --> pdb=" O   SER B 407 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLU B 420 " --> pdb=" O   TRP B 416 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE B 422 " --> pdb=" O   GLY B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 461
    Processing helix  chain 'B' and resid 466 through 489
      removed outlier: 3.712A  pdb=" N   LYS B 489 " --> pdb=" O   GLU B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 498
      removed outlier: 3.588A  pdb=" N   LEU B 498 " --> pdb=" O   GLU B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 515
      removed outlier: 3.652A  pdb=" N   LYS B 505 " --> pdb=" O   SER B 501 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY B 515 " --> pdb=" O   LYS B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 527
    Processing helix  chain 'B' and resid 529 through 533
      removed outlier: 3.680A  pdb=" N   TYR B 533 " --> pdb=" O   TYR B 530 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 418
      removed outlier: 3.686A  pdb=" N   GLU C 414 " --> pdb=" O   PRO C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 419 through 422
    Processing helix  chain 'C' and resid 430 through 442
    Processing helix  chain 'C' and resid 444 through 458
    Processing helix  chain 'C' and resid 484 through 494
      removed outlier: 3.515A  pdb=" N   ARG C 488 " --> pdb=" O   HIS C 484 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN C 494 " --> pdb=" O   LEU C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 499 through 503
    Processing helix  chain 'C' and resid 563 through 569
      removed outlier: 3.623A  pdb=" N   ILE C 566 " --> pdb=" O   PRO C 563 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 590 through 596
    Processing helix  chain 'C' and resid 612 through 617
      removed outlier: 4.252A  pdb=" N   GLN C 616 " --> pdb=" O   LEU C 612 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 643 through 648
    Processing helix  chain 'C' and resid 667 through 672
      removed outlier: 3.503A  pdb=" N   SER C 670 " --> pdb=" O   TYR C 667 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE C 672 " --> pdb=" O   ILE C 669 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 692 through 696
    Processing helix  chain 'C' and resid 714 through 720
    Processing helix  chain 'C' and resid 740 through 744
      removed outlier: 3.595A  pdb=" N   LEU C 744 " --> pdb=" O   ILE C 741 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 761 through 767
      removed outlier: 3.501A  pdb=" N   VAL C 764 " --> pdb=" O   PRO C 761 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU C 767 " --> pdb=" O   VAL C 764 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 775 through 784
      removed outlier: 4.559A  pdb=" N   LEU C 781 " --> pdb=" O   GLU C 777 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ARG C 784 " --> pdb=" O   LEU C 780 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 785 through 789
    Processing helix  chain 'C' and resid 803 through 808
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35
      removed outlier: 3.830A  pdb=" N   GLY A 121 " --> pdb=" O   VAL A 154 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   PHE A 179 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   VAL A 274 " --> pdb=" O   PHE A 179 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ASN A 181 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   SER A 276 " --> pdb=" O   ASN A 181 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   VAL A 183 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65
    Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 61
      removed outlier: 3.519A  pdb=" N   GLY B 144 " --> pdb=" O   ILE B 173 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR B 218 " --> pdb=" O   PHE B 198 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 87
      removed outlier: 3.548A  pdb=" N   PHE B 106 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 182
      removed outlier: 4.415A  pdb=" N   GLY B 181 " --> pdb=" O   LYS B 214 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 428 through 429
    Processing sheet with id=AA7, first strand: chain 'C' and resid 505 through 509
      removed outlier: 6.815A  pdb=" N   LEU C 528 " --> pdb=" O   VAL C 552 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   ASN C 554 " --> pdb=" O   LEU C 528 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ILE C 530 " --> pdb=" O   ASN C 554 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU C 551 " --> pdb=" O   THR C 576 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   THR C 578 " --> pdb=" O   LEU C 551 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LEU C 553 " --> pdb=" O   THR C 578 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU C 575 " --> pdb=" O   ARG C 603 " (cutoff:3.500A)
      removed outlier: 8.331A  pdb=" N   GLU C 605 " --> pdb=" O   LEU C 575 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE C 577 " --> pdb=" O   GLU C 605 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 559 through 561
      removed outlier: 6.395A  pdb=" N   ALA C 585 " --> pdb=" O   SER C 608 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 749 through 751
      removed outlier: 6.470A  pdb=" N   ILE C 750 " --> pdb=" O   LYS C 773 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   CYS C 774 " --> pdb=" O   GLN C 795 " (cutoff:3.500A)

    588 hydrogen bonds defined for protein.
    1629 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: 3.70

  Time building geometry restraints manager: 3.38 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: 3758
        1.34 -     1.45: 1949
        1.45 -     1.57: 6633
        1.57 -     1.69: 8
        1.69 -     1.81: 94
  Bond restraints: 12442
  Sorted by residual:
  bond pdb=" C4  ATP B 601 "
       pdb=" C5  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.448 -0.060 1.00e-02 1.00e+04 3.64e+01
  bond pdb=" C5  ATP B 601 "
       pdb=" N7  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.332  0.055 1.00e-02 1.00e+04 3.07e+01
  bond pdb=" C5  ATP B 601 "
       pdb=" C6  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.463 -0.054 1.00e-02 1.00e+04 2.87e+01
  bond pdb=" C4  ATP B 601 "
       pdb=" N9  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.374  1.324  0.050 1.00e-02 1.00e+04 2.55e+01
  bond pdb=" O3A APR A 701 "
       pdb=" PA  APR A 701 "
    ideal  model  delta    sigma   weight residual
    1.648  1.573  0.075 2.00e-02 2.50e+03 1.40e+01
  ... (remaining 12437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.01: 16573
        3.01 -     6.01: 199
        6.01 -     9.02: 23
        9.02 -    12.02: 2
       12.02 -    15.03: 2
  Bond angle restraints: 16799
  Sorted by residual:
  angle pdb=" PB  ATP B 601 "
        pdb=" O3B ATP B 601 "
        pdb=" PG  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     139.87  124.84   15.03 1.00e+00 1.00e+00 2.26e+02
  angle pdb=" PA  ATP B 601 "
        pdb=" O3A ATP B 601 "
        pdb=" PB  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     136.83  123.12   13.71 1.00e+00 1.00e+00 1.88e+02
  angle pdb=" C5  ATP B 601 "
        pdb=" C4  ATP B 601 "
        pdb=" N3  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     126.80  119.28    7.52 1.00e+00 1.00e+00 5.66e+01
  angle pdb=" N3  ATP B 601 "
        pdb=" C4  ATP B 601 "
        pdb=" N9  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     127.04  134.78   -7.74 1.15e+00 7.59e-01 4.54e+01
  angle pdb=" N1  ATP B 601 "
        pdb=" C2  ATP B 601 "
        pdb=" N3  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     128.69  122.80    5.89 1.00e+00 1.00e+00 3.47e+01
  ... (remaining 16794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6771
       17.91 -    35.82: 663
       35.82 -    53.73: 128
       53.73 -    71.63: 17
       71.63 -    89.54: 19
  Dihedral angle restraints: 7598
    sinusoidal: 3204
      harmonic: 4394
  Sorted by residual:
  dihedral pdb=" CA  HIS A 122 "
           pdb=" C   HIS A 122 "
           pdb=" N   SER A 123 "
           pdb=" CA  SER A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.22  -28.78     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  ALA B 145 "
           pdb=" C   ALA B 145 "
           pdb=" N   ALA B 146 "
           pdb=" CA  ALA B 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.66  -24.34     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  ILE B 163 "
           pdb=" C   ILE B 163 "
           pdb=" N   GLU B 164 "
           pdb=" CA  GLU B 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.64   21.36     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 7595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1243
       0.049 -    0.097: 497
       0.097 -    0.146: 108
       0.146 -    0.195: 7
       0.195 -    0.243: 1
  Chirality restraints: 1856
  Sorted by residual:
  chirality pdb=" CB  VAL B 317 "
            pdb=" CA  VAL B 317 "
            pdb=" CG1 VAL B 317 "
            pdb=" CG2 VAL B 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  THR B 162 "
            pdb=" CA  THR B 162 "
            pdb=" OG1 THR B 162 "
            pdb=" CG2 THR B 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  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   -2.52   -0.16 2.00e-01 2.50e+01 6.48e-01
  ... (remaining 1853 not shown)

  Planarity restraints: 2127
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 406 "   -0.025 2.00e-02 2.50e+03   3.18e-02 2.03e+01
        pdb=" CG  TYR A 406 "    0.074 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 406 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 406 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 406 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 406 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 406 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 406 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 321 "   -0.011 2.00e-02 2.50e+03   1.97e-02 7.74e+00
        pdb=" CG  TYR B 321 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 321 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 321 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 321 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 321 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 321 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 321 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 560 "    0.013 2.00e-02 2.50e+03   1.69e-02 5.70e+00
        pdb=" CG  TYR A 560 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 560 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 560 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 560 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 560 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 560 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 560 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 2124 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 313
        2.70 -     3.25: 11846
        3.25 -     3.80: 18253
        3.80 -     4.35: 24679
        4.35 -     4.90: 41059
  Nonbonded interactions: 96150
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 189 "
            pdb=" ND2 ASN B 195 "
     model   vdw
     2.145 3.120
  nonbonded pdb=" O   GLU A 322 "
            pdb=" OG  SER A 326 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O   LEU B 160 "
            pdb=" NH1 ARG B 194 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" O   LEU C 511 "
            pdb=" OG1 THR C 514 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OD2 ASP A 187 "
            pdb=" OH  TYR A 320 "
     model   vdw
     2.216 3.040
  ... (remaining 96145 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:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.620
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
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      :  0.008   0.075  12442  Z= 0.538
  Angle     :  0.911  15.030  16799  Z= 0.527
  Chirality :  0.051   0.243   1856
  Planarity :  0.006   0.053   2127
  Dihedral  : 15.153  89.542   4742
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.33 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.20), residues: 1483
  helix: -0.50 (0.19), residues: 719
  sheet: -0.11 (0.40), residues: 175
  loop : -1.79 (0.23), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 352 
 HIS   0.008   0.002   HIS B 409 
 PHE   0.022   0.003   PHE A 548 
 TYR   0.074   0.004   TYR A 406 
 ARG   0.021   0.001   ARG C 784 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.401 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.7886 (p0) cc_final: 0.7625 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.3171
  time to fit residues: 72.3180
Evaluate side-chains
  145 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 75 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 116 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 134 optimal weight:    5.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 333 ASN
B  33 HIS
B 195 ASN
B 457 GLN
C 483 GLN
C 795 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.167506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139181 restraints weight = 15045.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.09
r_work: 0.3271 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12442  Z= 0.190
  Angle     :  0.567   6.661  16799  Z= 0.307
  Chirality :  0.042   0.134   1856
  Planarity :  0.005   0.040   2127
  Dihedral  :  7.147  74.702   1699
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  5.44 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.21), residues: 1483
  helix:  0.40 (0.20), residues: 714
  sheet:  0.34 (0.40), residues: 176
  loop : -1.58 (0.22), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 352 
 HIS   0.004   0.001   HIS B 409 
 PHE   0.015   0.001   PHE B 290 
 TYR   0.029   0.002   TYR A 406 
 ARG   0.006   0.000   ARG C 784 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
REVERT: B  362 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7802 (ttt180)
REVERT: B  457 GLN cc_start: 0.7839 (tt0) cc_final: 0.7610 (tt0)
REVERT: C  616 GLN cc_start: 0.6284 (mm-40) cc_final: 0.5459 (pt0)
REVERT: C  785 LEU cc_start: 0.7753 (mt) cc_final: 0.7527 (mt)
  outliers start: 12
  outliers final: 7
  residues processed: 166
  average time/residue: 0.3227
  time to fit residues: 73.3787
Evaluate side-chains
  153 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue  468 THR
Chi-restraints excluded: chain C residue  478 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 143 optimal weight:    6.9990
   chunk 127 optimal weight:    5.9990
   chunk 147 optimal weight:    7.9990
   chunk 102 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 117 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 285 ASN
A 333 ASN
B  33 HIS
B 195 ASN
C 795 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.165917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.138673 restraints weight = 15319.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.05
r_work: 0.3255 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12442  Z= 0.247
  Angle     :  0.581   6.782  16799  Z= 0.311
  Chirality :  0.042   0.137   1856
  Planarity :  0.004   0.041   2127
  Dihedral  :  7.153  80.615   1699
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.94 %
    Favored  : 90.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.21), residues: 1483
  helix:  0.53 (0.19), residues: 717
  sheet:  0.55 (0.40), residues: 175
  loop : -1.56 (0.22), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 352 
 HIS   0.007   0.001   HIS B 409 
 PHE   0.015   0.002   PHE B 290 
 TYR   0.032   0.002   TYR A 406 
 ARG   0.006   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 HIS cc_start: 0.7710 (t-90) cc_final: 0.7279 (t70)
REVERT: B  457 GLN cc_start: 0.7841 (tt0) cc_final: 0.7596 (tt0)
  outliers start: 15
  outliers final: 10
  residues processed: 159
  average time/residue: 0.3072
  time to fit residues: 68.2103
Evaluate side-chains
  148 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue  468 THR
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  780 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 18 optimal weight:    0.0670
   chunk 91 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 131 optimal weight:    0.0370
   chunk 46 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
A 333 ASN
B  33 HIS
C 795 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.171410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.144948 restraints weight = 15112.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.90
r_work: 0.3279 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12442  Z= 0.129
  Angle     :  0.480   6.973  16799  Z= 0.258
  Chirality :  0.039   0.130   1856
  Planarity :  0.004   0.048   2127
  Dihedral  :  6.257  83.679   1699
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.26 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.21), residues: 1483
  helix:  0.91 (0.20), residues: 718
  sheet:  0.68 (0.38), residues: 190
  loop : -1.36 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 352 
 HIS   0.007   0.001   HIS B  33 
 PHE   0.012   0.001   PHE B  97 
 TYR   0.013   0.001   TYR A 406 
 ARG   0.008   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 1.521 
Fit side-chains
REVERT: A  206 HIS cc_start: 0.7764 (t-90) cc_final: 0.7295 (t70)
REVERT: A  246 GLU cc_start: 0.6751 (pt0) cc_final: 0.6492 (pt0)
REVERT: B  295 LYS cc_start: 0.8707 (tppt) cc_final: 0.8350 (mttp)
REVERT: B  457 GLN cc_start: 0.7673 (tt0) cc_final: 0.7306 (tt0)
REVERT: C  671 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.6886 (mp0)
REVERT: C  748 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6622 (mmmt)
REVERT: C  785 LEU cc_start: 0.7917 (mt) cc_final: 0.7537 (mt)
REVERT: C  798 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6946 (pt0)
  outliers start: 15
  outliers final: 7
  residues processed: 173
  average time/residue: 0.3002
  time to fit residues: 72.7884
Evaluate side-chains
  152 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  671 GLU
Chi-restraints excluded: chain C residue  780 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    0.3980
   chunk 12 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 128 optimal weight:    7.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
A 476 HIS
B  33 HIS
C 471 HIS
C 795 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.167764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.140155 restraints weight = 15137.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.15
r_work: 0.3213 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12442  Z= 0.208
  Angle     :  0.533   6.540  16799  Z= 0.283
  Chirality :  0.041   0.135   1856
  Planarity :  0.004   0.045   2127
  Dihedral  :  6.598  84.683   1699
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 10.95 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.22), residues: 1483
  helix:  0.97 (0.20), residues: 718
  sheet:  0.82 (0.39), residues: 188
  loop : -1.34 (0.23), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 158 
 HIS   0.007   0.001   HIS B 409 
 PHE   0.018   0.002   PHE B 290 
 TYR   0.024   0.002   TYR A 406 
 ARG   0.010   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 1.392 
Fit side-chains
REVERT: A  206 HIS cc_start: 0.7571 (t-90) cc_final: 0.7028 (t70)
REVERT: A  246 GLU cc_start: 0.6785 (pt0) cc_final: 0.6448 (pt0)
REVERT: B  295 LYS cc_start: 0.8598 (tppt) cc_final: 0.8252 (mttp)
REVERT: C  671 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.6701 (mp0)
REVERT: C  748 LYS cc_start: 0.6941 (mmtt) cc_final: 0.6545 (mmmt)
REVERT: C  798 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6852 (pt0)
  outliers start: 16
  outliers final: 12
  residues processed: 161
  average time/residue: 0.3003
  time to fit residues: 67.4994
Evaluate side-chains
  153 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue  468 THR
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  543 MET
Chi-restraints excluded: chain C residue  574 VAL
Chi-restraints excluded: chain C residue  671 GLU
Chi-restraints excluded: chain C residue  780 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 144 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 145 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 140 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
A 333 ASN
B  33 HIS
B 457 GLN
C 795 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.170349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.142611 restraints weight = 15265.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.15
r_work: 0.3273 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12442  Z= 0.138
  Angle     :  0.482   6.669  16799  Z= 0.257
  Chirality :  0.039   0.131   1856
  Planarity :  0.004   0.048   2127
  Dihedral  :  6.265  84.415   1699
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.68 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.22), residues: 1483
  helix:  1.09 (0.20), residues: 719
  sheet:  0.83 (0.39), residues: 190
  loop : -1.21 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 352 
 HIS   0.005   0.001   HIS B  33 
 PHE   0.011   0.001   PHE B  97 
 TYR   0.015   0.001   TYR A 406 
 ARG   0.009   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 1.424 
Fit side-chains
REVERT: A  206 HIS cc_start: 0.7807 (t-90) cc_final: 0.7385 (t70)
REVERT: A  246 GLU cc_start: 0.6871 (pt0) cc_final: 0.6663 (pt0)
REVERT: B  295 LYS cc_start: 0.8674 (tppt) cc_final: 0.8307 (mttp)
REVERT: C  671 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.6627 (mp0)
REVERT: C  748 LYS cc_start: 0.6902 (mmtt) cc_final: 0.6609 (mmmt)
REVERT: C  798 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7007 (pt0)
  outliers start: 19
  outliers final: 13
  residues processed: 160
  average time/residue: 0.2892
  time to fit residues: 65.4730
Evaluate side-chains
  150 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  574 VAL
Chi-restraints excluded: chain C residue  609 ILE
Chi-restraints excluded: chain C residue  671 GLU
Chi-restraints excluded: chain C residue  780 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 96 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 132 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 210 GLN
A 285 ASN
A 333 ASN
B  33 HIS
C 795 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.170459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.143693 restraints weight = 15142.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.06
r_work: 0.3274 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12442  Z= 0.139
  Angle     :  0.482   6.711  16799  Z= 0.256
  Chirality :  0.039   0.129   1856
  Planarity :  0.004   0.048   2127
  Dihedral  :  6.163  83.979   1699
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.05 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.22), residues: 1483
  helix:  1.20 (0.20), residues: 720
  sheet:  0.96 (0.39), residues: 190
  loop : -1.11 (0.23), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 352 
 HIS   0.006   0.001   HIS B  33 
 PHE   0.022   0.001   PHE B 290 
 TYR   0.015   0.001   TYR A 406 
 ARG   0.012   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 1.355 
Fit side-chains
REVERT: A  206 HIS cc_start: 0.7816 (t-90) cc_final: 0.7369 (t70)
REVERT: A  246 GLU cc_start: 0.6733 (pt0) cc_final: 0.6496 (pt0)
REVERT: A  327 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7873 (ttt)
REVERT: B  295 LYS cc_start: 0.8632 (tppt) cc_final: 0.8234 (mttp)
REVERT: C  671 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.6557 (mp0)
REVERT: C  748 LYS cc_start: 0.6907 (mmtt) cc_final: 0.6610 (mmmt)
REVERT: C  798 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7044 (pt0)
  outliers start: 19
  outliers final: 15
  residues processed: 151
  average time/residue: 0.2768
  time to fit residues: 58.5461
Evaluate side-chains
  151 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain C residue  468 THR
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  548 VAL
Chi-restraints excluded: chain C residue  574 VAL
Chi-restraints excluded: chain C residue  609 ILE
Chi-restraints excluded: chain C residue  671 GLU
Chi-restraints excluded: chain C residue  780 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 210 GLN
A 285 ASN
A 333 ASN
B  33 HIS
C 795 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.170466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.144309 restraints weight = 15258.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.12
r_work: 0.3275 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12442  Z= 0.147
  Angle     :  0.484   6.739  16799  Z= 0.258
  Chirality :  0.039   0.130   1856
  Planarity :  0.004   0.047   2127
  Dihedral  :  6.165  84.286   1699
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.98 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.22), residues: 1483
  helix:  1.23 (0.20), residues: 719
  sheet:  1.03 (0.39), residues: 190
  loop : -1.07 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 352 
 HIS   0.006   0.001   HIS B  33 
 PHE   0.011   0.001   PHE A 548 
 TYR   0.016   0.001   TYR A 406 
 ARG   0.011   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 1.478 
Fit side-chains
REVERT: A  206 HIS cc_start: 0.7803 (t-90) cc_final: 0.7339 (t70)
REVERT: A  246 GLU cc_start: 0.6729 (pt0) cc_final: 0.6497 (pt0)
REVERT: A  327 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7896 (ttt)
REVERT: B  295 LYS cc_start: 0.8630 (tppt) cc_final: 0.8247 (mttp)
REVERT: C  671 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.6632 (mp0)
REVERT: C  748 LYS cc_start: 0.6893 (mmtt) cc_final: 0.6600 (mmmt)
REVERT: C  798 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7025 (pt0)
  outliers start: 23
  outliers final: 15
  residues processed: 156
  average time/residue: 0.2766
  time to fit residues: 61.3636
Evaluate side-chains
  151 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain C residue  468 THR
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  548 VAL
Chi-restraints excluded: chain C residue  574 VAL
Chi-restraints excluded: chain C residue  671 GLU
Chi-restraints excluded: chain C residue  780 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 120 optimal weight:   20.0000
   chunk 100 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 85 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 210 GLN
A 285 ASN
A 333 ASN
B  33 HIS
B 457 GLN
C 795 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.167897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.139846 restraints weight = 15135.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.16
r_work: 0.3246 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12442  Z= 0.202
  Angle     :  0.531   6.432  16799  Z= 0.281
  Chirality :  0.041   0.136   1856
  Planarity :  0.004   0.045   2127
  Dihedral  :  6.532  85.353   1699
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.27 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.22), residues: 1483
  helix:  1.12 (0.20), residues: 720
  sheet:  1.09 (0.39), residues: 188
  loop : -1.07 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 352 
 HIS   0.006   0.001   HIS B 409 
 PHE   0.023   0.001   PHE B 290 
 TYR   0.022   0.002   TYR A 406 
 ARG   0.012   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 1.441 
Fit side-chains
REVERT: A  206 HIS cc_start: 0.7805 (t-90) cc_final: 0.7350 (t70)
REVERT: A  246 GLU cc_start: 0.7048 (pt0) cc_final: 0.6810 (pt0)
REVERT: A  327 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7944 (ttt)
REVERT: B  295 LYS cc_start: 0.8698 (tppt) cc_final: 0.8373 (mttp)
REVERT: C  671 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.6823 (mp0)
REVERT: C  748 LYS cc_start: 0.6976 (mmtt) cc_final: 0.6691 (mmmt)
REVERT: C  798 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7091 (pt0)
  outliers start: 20
  outliers final: 15
  residues processed: 157
  average time/residue: 0.2738
  time to fit residues: 60.7824
Evaluate side-chains
  154 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  457 GLN
Chi-restraints excluded: chain C residue  468 THR
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  548 VAL
Chi-restraints excluded: chain C residue  574 VAL
Chi-restraints excluded: chain C residue  671 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 65 optimal weight:    0.3980
   chunk 126 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 210 GLN
A 285 ASN
A 333 ASN
B 457 GLN
C 795 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.168719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.141160 restraints weight = 15119.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.15
r_work: 0.3223 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12442  Z= 0.178
  Angle     :  0.518   6.387  16799  Z= 0.274
  Chirality :  0.040   0.130   1856
  Planarity :  0.004   0.051   2127
  Dihedral  :  6.443  85.420   1699
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.42 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.22), residues: 1483
  helix:  1.16 (0.20), residues: 719
  sheet:  1.02 (0.39), residues: 190
  loop : -1.03 (0.24), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 352 
 HIS   0.005   0.001   HIS B 409 
 PHE   0.012   0.001   PHE A 548 
 TYR   0.019   0.001   TYR A 406 
 ARG   0.013   0.000   ARG A 100 

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

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

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2966 Ramachandran restraints generated.
    1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 1.529 
Fit side-chains
REVERT: A  206 HIS cc_start: 0.7630 (t-90) cc_final: 0.7094 (t70)
REVERT: A  246 GLU cc_start: 0.6705 (pt0) cc_final: 0.6429 (pt0)
REVERT: A  320 TYR cc_start: 0.8210 (m-80) cc_final: 0.7655 (m-80)
REVERT: A  327 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7920 (ttt)
REVERT: B  295 LYS cc_start: 0.8516 (tppt) cc_final: 0.8210 (mttp)
REVERT: C  671 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.6601 (mp0)
REVERT: C  748 LYS cc_start: 0.6893 (mmtt) cc_final: 0.6530 (mmmt)
REVERT: C  798 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6938 (pt0)
  outliers start: 21
  outliers final: 16
  residues processed: 156
  average time/residue: 0.2907
  time to fit residues: 63.7752
Evaluate side-chains
  155 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  457 GLN
Chi-restraints excluded: chain C residue  468 THR
Chi-restraints excluded: chain C residue  478 ASP
Chi-restraints excluded: chain C residue  548 VAL
Chi-restraints excluded: chain C residue  574 VAL
Chi-restraints excluded: chain C residue  671 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 129 optimal weight:    0.0020
   chunk 5 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 33 optimal weight:    0.3980
   chunk 122 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 144 optimal weight:    5.9990
   chunk 146 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 210 GLN
A 285 ASN
A 292 GLN
A 333 ASN
B  33 HIS
B 457 GLN
C 795 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.170861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.143744 restraints weight = 15135.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.04
r_work: 0.3316 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12442  Z= 0.136
  Angle     :  0.488   6.673  16799  Z= 0.262
  Chirality :  0.040   0.195   1856
  Planarity :  0.004   0.056   2127
  Dihedral  :  6.154  85.166   1699
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.71 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.22), residues: 1483
  helix:  1.25 (0.20), residues: 719
  sheet:  1.04 (0.40), residues: 190
  loop : -0.96 (0.24), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 352 
 HIS   0.005   0.001   HIS B  33 
 PHE   0.023   0.001   PHE B 290 
 TYR   0.013   0.001   TYR A 406 
 ARG   0.013   0.000   ARG A 100 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5175.31 seconds
wall clock time: 92 minutes 40.66 seconds (5560.66 seconds total)