Starting phenix.real_space_refine
on Sat May  2 22:40:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rgn_19135/05_2026/8rgn_19135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rgn_19135/05_2026/8rgn_19135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rgn_19135/05_2026/8rgn_19135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rgn_19135/05_2026/8rgn_19135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rgn_19135/05_2026/8rgn_19135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rgn_19135/05_2026/8rgn_19135.cif"
  }
  resolution = 3.7
  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=   0.001 sd=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    5782      2.51       5
     N    1498      2.21       5
     O    1707      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 9031
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4448
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 17, 'TRANS': 560}
    Chain: "B"
      Number of atoms: 4448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4448
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 17, 'TRANS': 560}
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 65
          Unusual residues: {' MG': 1, 'ATP': 1, 'RHQ': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 65
          Unusual residues: {' MG': 1, 'ATP': 1, 'RHQ': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.44, per 1000 atoms: 0.27
  Number of scatterers: 9031
  At special positions: 0
  Unit cell: (85.212, 76.796, 135.708, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       6     15.00
     Mg      2     11.99
     O    1707      8.00
     N    1498      7.00
     C    5782      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=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 327.3 milliseconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      68.0% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 21
    Processing helix  chain 'A' and resid 22 through 26
    Processing helix  chain 'A' and resid 27 through 57
      removed outlier: 4.396A  pdb=" N   PHE A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      Proline residue:  A  47  - end of helix
      removed outlier: 4.793A  pdb=" N   GLN A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
      removed outlier: 3.913A  pdb=" N   GLN A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 107
      removed outlier: 3.769A  pdb=" N   ALA A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   PHE A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA A  82 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR A  83 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ALA A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 118
      removed outlier: 4.011A  pdb=" N   PHE A 115 " --> pdb=" O   PRO A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 129
      removed outlier: 3.953A  pdb=" N   THR A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   SER A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 3.503A  pdb=" N   VAL A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   GLU A 136 " --> pdb=" O   MET A 132 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   LEU A 137 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 165 through 210
      Proline residue:  A 175  - end of helix
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 212 through 220
    Processing helix  chain 'A' and resid 221 through 248
      removed outlier: 3.887A  pdb=" N   GLY A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER A 235 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ALA A 244 " --> pdb=" O   GLY A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 273
      removed outlier: 3.530A  pdb=" N   ILE A 254 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 315
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 380 through 388
    Processing helix  chain 'A' and resid 406 through 409
      removed outlier: 5.941A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 406 through 409'
    Processing helix  chain 'A' and resid 410 through 415
      removed outlier: 3.606A  pdb=" N   GLU A 415 " --> pdb=" O   GLU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 453
    Processing helix  chain 'A' and resid 459 through 464
      removed outlier: 3.934A  pdb=" N   GLU A 463 " --> pdb=" O   ASN A 459 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU A 464 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 459 through 464'
    Processing helix  chain 'A' and resid 473 through 477
    Processing helix  chain 'A' and resid 482 through 495
      removed outlier: 4.126A  pdb=" N   ARG A 495 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 525
    Processing helix  chain 'A' and resid 536 through 540
      removed outlier: 3.505A  pdb=" N   VAL A 540 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 567
    Processing helix  chain 'A' and resid 567 through 585
      removed outlier: 3.517A  pdb=" N   ARG A 571 " --> pdb=" O   HIS A 567 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASP A 572 " --> pdb=" O   GLY A 568 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLN A 577 " --> pdb=" O   PHE A 573 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLU A 585 " --> pdb=" O   ASN A 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 21
    Processing helix  chain 'B' and resid 22 through 26
    Processing helix  chain 'B' and resid 27 through 57
      removed outlier: 4.396A  pdb=" N   PHE B  31 " --> pdb=" O   GLY B  27 " (cutoff:3.500A)
      Proline residue:  B  47  - end of helix
      removed outlier: 4.793A  pdb=" N   GLN B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 66
      removed outlier: 3.913A  pdb=" N   GLN B  66 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 107
      removed outlier: 3.769A  pdb=" N   ALA B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   PHE B  75 " --> pdb=" O   ALA B  71 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR B  83 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ALA B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 118
      removed outlier: 4.011A  pdb=" N   PHE B 115 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 129
      removed outlier: 4.050A  pdb=" N   THR B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 140
      removed outlier: 3.502A  pdb=" N   VAL B 134 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   GLU B 136 " --> pdb=" O   MET B 132 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   LEU B 137 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE B 138 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
    Processing helix  chain 'B' and resid 165 through 210
      Proline residue:  B 175  - end of helix
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 221 through 248
      removed outlier: 3.888A  pdb=" N   GLY B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER B 235 " --> pdb=" O   MET B 231 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU B 239 " --> pdb=" O   SER B 235 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLU B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ALA B 244 " --> pdb=" O   GLY B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 273
      removed outlier: 3.529A  pdb=" N   ILE B 254 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 255 " --> pdb=" O   GLY B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 315
      Proline residue:  B 296  - end of helix
    Processing helix  chain 'B' and resid 380 through 388
    Processing helix  chain 'B' and resid 406 through 409
      removed outlier: 5.940A  pdb=" N   SER B 409 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 406 through 409'
    Processing helix  chain 'B' and resid 410 through 415
      removed outlier: 3.606A  pdb=" N   GLU B 415 " --> pdb=" O   GLU B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 455
    Processing helix  chain 'B' and resid 473 through 477
    Processing helix  chain 'B' and resid 482 through 495
      removed outlier: 4.125A  pdb=" N   ARG B 495 " --> pdb=" O   ARG B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 525
    Processing helix  chain 'B' and resid 536 through 540
      removed outlier: 3.505A  pdb=" N   VAL B 540 " --> pdb=" O   LEU B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 567
    Processing helix  chain 'B' and resid 567 through 585
      removed outlier: 3.517A  pdb=" N   ARG B 571 " --> pdb=" O   HIS B 567 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASP B 572 " --> pdb=" O   GLY B 568 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLN B 577 " --> pdb=" O   PHE B 573 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLU B 585 " --> pdb=" O   ASN B 581 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348
      removed outlier: 7.702A  pdb=" N   PHE A 348 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   LYS A 358 " --> pdb=" O   PHE A 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 420
      removed outlier: 6.573A  pdb=" N   GLY A 418 " --> pdb=" O   MET A 501 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU A 500 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   LEU A 502 " --> pdb=" O   ILE A 533 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   VAL A 369 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   LEU A 547 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ALA A 371 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   VAL A 549 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY A 556 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   GLU A 550 " --> pdb=" O   ILE A 554 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   ILE A 554 " --> pdb=" O   GLU A 550 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 363 through 364
    Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 348
      removed outlier: 5.155A  pdb=" N   VAL B 346 " --> pdb=" O   GLU B 359 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   GLU B 359 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 420
      removed outlier: 6.573A  pdb=" N   GLY B 418 " --> pdb=" O   MET B 501 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU B 500 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   ILE B 533 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   LEU B 502 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL B 369 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   LEU B 547 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   VAL B 549 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY B 556 " --> pdb=" O   PHE B 548 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   GLU B 550 " --> pdb=" O   ILE B 554 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   ILE B 554 " --> pdb=" O   GLU B 550 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1572 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: 1.45

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1489
        1.31 -     1.44: 2241
        1.44 -     1.56: 5356
        1.56 -     1.69: 12
        1.69 -     1.81: 70
  Bond restraints: 9168
  Sorted by residual:
  bond pdb=" C4  ATP B 602 "
       pdb=" C5  ATP B 602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.465 -0.077 1.00e-02 1.00e+04 5.87e+01
  bond pdb=" C4  ATP A 602 "
       pdb=" C5  ATP A 602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.463 -0.075 1.00e-02 1.00e+04 5.68e+01
  bond pdb=" C5  RHQ A 601 "
       pdb=" N2  RHQ A 601 "
    ideal  model  delta    sigma   weight residual
    1.436  1.308  0.128 2.00e-02 2.50e+03 4.07e+01
  bond pdb=" C5  RHQ B 601 "
       pdb=" N2  RHQ B 601 "
    ideal  model  delta    sigma   weight residual
    1.436  1.308  0.128 2.00e-02 2.50e+03 4.07e+01
  bond pdb=" C5  ATP A 602 "
       pdb=" C6  ATP A 602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.473 -0.064 1.00e-02 1.00e+04 4.04e+01
  ... (remaining 9163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.09: 12383
        9.09 -    18.18: 25
       18.18 -    27.26: 13
       27.26 -    36.35: 4
       36.35 -    45.44: 1
  Bond angle restraints: 12426
  Sorted by residual:
  angle pdb=" N   THR B 470 "
        pdb=" CA  THR B 470 "
        pdb=" C   THR B 470 "
      ideal   model   delta    sigma   weight residual
     108.26   62.82   45.44 1.66e+00 3.63e-01 7.49e+02
  angle pdb=" PB  ATP A 602 "
        pdb=" O3B ATP A 602 "
        pdb=" PG  ATP A 602 "
      ideal   model   delta    sigma   weight residual
     139.87  116.11   23.76 1.00e+00 1.00e+00 5.64e+02
  angle pdb=" PB  ATP B 602 "
        pdb=" O3B ATP B 602 "
        pdb=" PG  ATP B 602 "
      ideal   model   delta    sigma   weight residual
     139.87  116.45   23.42 1.00e+00 1.00e+00 5.49e+02
  angle pdb=" PA  ATP B 602 "
        pdb=" O3A ATP B 602 "
        pdb=" PB  ATP B 602 "
      ideal   model   delta    sigma   weight residual
     136.83  116.32   20.51 1.00e+00 1.00e+00 4.21e+02
  angle pdb=" PA  ATP A 602 "
        pdb=" O3A ATP A 602 "
        pdb=" PB  ATP A 602 "
      ideal   model   delta    sigma   weight residual
     136.83  116.59   20.24 1.00e+00 1.00e+00 4.10e+02
  ... (remaining 12421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 4790
       17.12 -    34.24: 612
       34.24 -    51.36: 106
       51.36 -    68.49: 31
       68.49 -    85.61: 17
  Dihedral angle restraints: 5556
    sinusoidal: 2244
      harmonic: 3312
  Sorted by residual:
  dihedral pdb=" N   ALA B 119 "
           pdb=" C   ALA B 119 "
           pdb=" CA  ALA B 119 "
           pdb=" CB  ALA B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90   91.21   31.69     0      2.50e+00 1.60e-01 1.61e+02
  dihedral pdb=" C   VAL A 443 "
           pdb=" N   VAL A 443 "
           pdb=" CA  VAL A 443 "
           pdb=" CB  VAL A 443 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00  -90.47  -31.53     0      2.50e+00 1.60e-01 1.59e+02
  dihedral pdb=" N   ALA A 119 "
           pdb=" C   ALA A 119 "
           pdb=" CA  ALA A 119 "
           pdb=" CB  ALA A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90   93.28   29.62     0      2.50e+00 1.60e-01 1.40e+02
  ... (remaining 5553 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.248: 1471
       0.248 -    0.495: 12
       0.495 -    0.743: 1
       0.743 -    0.990: 1
       0.990 -    1.238: 1
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CA  ASN B 466 "
            pdb=" N   ASN B 466 "
            pdb=" C   ASN B 466 "
            pdb=" CB  ASN B 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.27    1.24 2.00e-01 2.50e+01 3.83e+01
  chirality pdb=" CA  ASN A 466 "
            pdb=" N   ASN A 466 "
            pdb=" C   ASN A 466 "
            pdb=" CB  ASN A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.57    0.94 2.00e-01 2.50e+01 2.20e+01
  chirality pdb=" CA  VAL A 443 "
            pdb=" N   VAL A 443 "
            pdb=" C   VAL A 443 "
            pdb=" CB  VAL A 443 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    3.02   -0.58 2.00e-01 2.50e+01 8.38e+00
  ... (remaining 1483 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  RHQ B 601 "   -0.057 2.00e-02 2.50e+03   2.04e-01 1.15e+03
        pdb=" C2  RHQ B 601 "    0.075 2.00e-02 2.50e+03
        pdb=" C21 RHQ B 601 "   -0.034 2.00e-02 2.50e+03
        pdb=" C24 RHQ B 601 "    0.499 2.00e-02 2.50e+03
        pdb=" C3  RHQ B 601 "    0.082 2.00e-02 2.50e+03
        pdb=" C4  RHQ B 601 "   -0.045 2.00e-02 2.50e+03
        pdb=" C5  RHQ B 601 "   -0.167 2.00e-02 2.50e+03
        pdb=" C6  RHQ B 601 "   -0.186 2.00e-02 2.50e+03
        pdb=" C9  RHQ B 601 "    0.192 2.00e-02 2.50e+03
        pdb=" N2  RHQ B 601 "   -0.297 2.00e-02 2.50e+03
        pdb=" O1  RHQ B 601 "   -0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  RHQ A 601 "    0.057 2.00e-02 2.50e+03   2.04e-01 1.15e+03
        pdb=" C2  RHQ A 601 "   -0.075 2.00e-02 2.50e+03
        pdb=" C21 RHQ A 601 "    0.035 2.00e-02 2.50e+03
        pdb=" C24 RHQ A 601 "   -0.499 2.00e-02 2.50e+03
        pdb=" C3  RHQ A 601 "   -0.082 2.00e-02 2.50e+03
        pdb=" C4  RHQ A 601 "    0.045 2.00e-02 2.50e+03
        pdb=" C5  RHQ A 601 "    0.168 2.00e-02 2.50e+03
        pdb=" C6  RHQ A 601 "    0.186 2.00e-02 2.50e+03
        pdb=" C9  RHQ A 601 "   -0.191 2.00e-02 2.50e+03
        pdb=" N2  RHQ A 601 "    0.297 2.00e-02 2.50e+03
        pdb=" O1  RHQ A 601 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 443 "    0.021 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   VAL A 443 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   VAL A 443 "    0.028 2.00e-02 2.50e+03
        pdb=" N   THR A 444 "    0.026 2.00e-02 2.50e+03
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.50: 115
        2.50 -     3.10: 7534
        3.10 -     3.70: 13676
        3.70 -     4.30: 19338
        4.30 -     4.90: 31073
  Nonbonded interactions: 71736
  Sorted by model distance:
  nonbonded pdb=" N   THR B 470 "
            pdb=" O   THR B 470 "
     model   vdw
     1.895 2.496
  nonbonded pdb=" O2G ATP A 602 "
            pdb="MG    MG A 603 "
     model   vdw
     1.950 2.170
  nonbonded pdb=" O2G ATP B 602 "
            pdb="MG    MG B 603 "
     model   vdw
     1.960 2.170
  nonbonded pdb=" O2B ATP B 602 "
            pdb="MG    MG B 603 "
     model   vdw
     1.961 2.170
  nonbonded pdb=" O2B ATP A 602 "
            pdb="MG    MG A 603 "
     model   vdw
     1.962 2.170
  ... (remaining 71731 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
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:             1.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.270
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
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   0.128   9168  Z= 0.465
  Angle     :  1.548  45.440  12426  Z= 1.026
  Chirality :  0.072   1.238   1486
  Planarity :  0.009   0.204   1546
  Dihedral  : 16.175  85.607   3428
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 30.90
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.25 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  8.52 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.94 %
  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: -3.15 (0.21), residues: 1152
  helix: -1.53 (0.17), residues: 688
  sheet: -3.52 (0.51), residues: 36
  loop : -2.74 (0.24), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 432 
 TYR   0.014   0.002   TYR B 419 
 PHE   0.026   0.002   PHE B 384 
 TRP   0.016   0.002   TRP A 104 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00798 ( 9168)
  covalent geometry    : angle       1.54842 (12426)
  hydrogen bonds       : bond        0.18880 (  540)
  hydrogen bonds       : angle       7.89889 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 181
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ILE cc_start: 0.8282 (tp) cc_final: 0.8052 (tt)
REVERT: A  295 MET cc_start: 0.8426 (tmm) cc_final: 0.8186 (tmm)
REVERT: A  299 GLN cc_start: 0.7861 (tp40) cc_final: 0.7592 (tp40)
REVERT: A  433 GLU cc_start: 0.7848 (tp30) cc_final: 0.7008 (tm-30)
REVERT: A  449 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7953 (mm-30)
REVERT: A  467 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8078 (mt0)
REVERT: A  510 ASP cc_start: 0.6809 (p0) cc_final: 0.6576 (p0)
REVERT: B  180 ILE cc_start: 0.8334 (tp) cc_final: 0.8116 (tt)
REVERT: B  259 MET cc_start: 0.8641 (tpp) cc_final: 0.8355 (mmt)
REVERT: B  299 GLN cc_start: 0.7917 (tp40) cc_final: 0.7706 (tp40)
REVERT: B  433 GLU cc_start: 0.7910 (tp30) cc_final: 0.7042 (tm-30)
REVERT: B  510 ASP cc_start: 0.6842 (p0) cc_final: 0.6573 (p0)
REVERT: B  580 MET cc_start: 0.7191 (mmp) cc_final: 0.6420 (mmp)
  outliers start: 8
  outliers final: 2
  residues processed: 187
  average time/residue: 0.1084
  time to fit residues: 27.1803
Evaluate side-chains
  130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  467 GLN
Chi-restraints excluded: chain B residue  467 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 100 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
B 581 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.197787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.147028 restraints weight = 11233.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.151857 restraints weight = 6716.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.154779 restraints weight = 5081.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.156090 restraints weight = 4368.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.156961 restraints weight = 4052.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
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      :  0.004   0.039   9168  Z= 0.199
  Angle     :  0.748   7.417  12426  Z= 0.388
  Chirality :  0.045   0.143   1486
  Planarity :  0.005   0.044   1546
  Dihedral  : 10.826  76.054   1329
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.64 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.45 %
    Favored  : 80.60 %
  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 (0.24), residues: 1152
  helix: -0.00 (0.19), residues: 724
  sheet: -2.48 (0.60), residues: 34
  loop : -2.25 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 399 
 TYR   0.018   0.002   TYR B 419 
 PHE   0.023   0.002   PHE A 468 
 TRP   0.007   0.001   TRP B 104 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 9168)
  covalent geometry    : angle       0.74761 (12426)
  hydrogen bonds       : bond        0.06487 (  540)
  hydrogen bonds       : angle       5.50615 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8737 (t) cc_final: 0.8186 (p)
REVERT: A  139 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8717 (m)
REVERT: A  433 GLU cc_start: 0.7627 (tp30) cc_final: 0.6844 (tm-30)
REVERT: A  567 HIS cc_start: 0.7591 (t-90) cc_final: 0.7380 (t70)
REVERT: B   36 SER cc_start: 0.8755 (t) cc_final: 0.8218 (p)
REVERT: B  139 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8720 (m)
REVERT: B  162 MET cc_start: 0.8888 (mmm) cc_final: 0.8587 (mmm)
REVERT: B  433 GLU cc_start: 0.7617 (tp30) cc_final: 0.6886 (tm-30)
REVERT: B  510 ASP cc_start: 0.6564 (p0) cc_final: 0.6144 (p0)
REVERT: B  538 SER cc_start: 0.8559 (p) cc_final: 0.7711 (t)
  outliers start: 19
  outliers final: 10
  residues processed: 139
  average time/residue: 0.0871
  time to fit residues: 17.5401
Evaluate side-chains
  129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    0.2980
   chunk 54 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
A 577 GLN
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.190293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.155560 restraints weight = 10429.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.153163 restraints weight = 14134.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.155373 restraints weight = 12946.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.155514 restraints weight = 9128.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155664 restraints weight = 8434.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9168  Z= 0.175
  Angle     :  0.672   8.373  12426  Z= 0.346
  Chirality :  0.042   0.139   1486
  Planarity :  0.004   0.039   1546
  Dihedral  :  9.847  74.718   1323
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.90 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.71 %
    Favored  : 76.59 %
  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: -0.52 (0.25), residues: 1152
  helix:  0.61 (0.20), residues: 720
  sheet: -1.36 (0.59), residues: 58
  loop : -2.01 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 571 
 TYR   0.014   0.001   TYR A 419 
 PHE   0.015   0.001   PHE B 291 
 TRP   0.007   0.001   TRP B 104 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9168)
  covalent geometry    : angle       0.67238 (12426)
  hydrogen bonds       : bond        0.05503 (  540)
  hydrogen bonds       : angle       4.96656 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8500 (t) cc_final: 0.8224 (p)
REVERT: A  386 LEU cc_start: 0.8917 (tp) cc_final: 0.8581 (tt)
REVERT: A  433 GLU cc_start: 0.7253 (tp30) cc_final: 0.6846 (tm-30)
REVERT: A  536 ARG cc_start: 0.7303 (mtt-85) cc_final: 0.7027 (mtt90)
REVERT: B   36 SER cc_start: 0.8455 (t) cc_final: 0.8202 (p)
REVERT: B  510 ASP cc_start: 0.6560 (p0) cc_final: 0.6178 (p0)
REVERT: B  580 MET cc_start: 0.7278 (tpp) cc_final: 0.6905 (tpp)
  outliers start: 36
  outliers final: 18
  residues processed: 151
  average time/residue: 0.0879
  time to fit residues: 19.1859
Evaluate side-chains
  128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 24 optimal weight:    0.0050
   chunk 9 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0170
   chunk 99 optimal weight:    0.0470
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.2930

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
A 567 HIS
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.194907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.158071 restraints weight = 10524.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.156759 restraints weight = 10506.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.158957 restraints weight = 9683.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.159221 restraints weight = 7342.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.159177 restraints weight = 6838.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9168  Z= 0.135
  Angle     :  0.634   9.282  12426  Z= 0.322
  Chirality :  0.041   0.144   1486
  Planarity :  0.003   0.040   1546
  Dihedral  :  9.412  84.019   1322
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.38 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.97 %
    Favored  : 74.54 %
  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: -0.06 (0.25), residues: 1152
  helix:  0.90 (0.20), residues: 724
  sheet: -0.97 (0.64), residues: 58
  loop : -1.74 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 571 
 TYR   0.011   0.001   TYR A 268 
 PHE   0.014   0.001   PHE B 291 
 TRP   0.005   0.001   TRP B 164 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9168)
  covalent geometry    : angle       0.63417 (12426)
  hydrogen bonds       : bond        0.05056 (  540)
  hydrogen bonds       : angle       4.65162 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8792 (t) cc_final: 0.8414 (p)
REVERT: A  386 LEU cc_start: 0.8856 (tp) cc_final: 0.8562 (tt)
REVERT: B   36 SER cc_start: 0.8753 (t) cc_final: 0.8406 (p)
REVERT: B  510 ASP cc_start: 0.6522 (p0) cc_final: 0.6112 (p0)
REVERT: B  580 MET cc_start: 0.7367 (tpp) cc_final: 0.7147 (tpp)
  outliers start: 34
  outliers final: 17
  residues processed: 147
  average time/residue: 0.0875
  time to fit residues: 18.5812
Evaluate side-chains
  125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   chunk 26 optimal weight:   20.0000
   chunk 74 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.197100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.160444 restraints weight = 10427.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.158381 restraints weight = 11346.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.161423 restraints weight = 10550.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.161444 restraints weight = 7550.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.161325 restraints weight = 7263.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9168  Z= 0.145
  Angle     :  0.645   9.956  12426  Z= 0.323
  Chirality :  0.042   0.232   1486
  Planarity :  0.003   0.041   1546
  Dihedral  :  9.219  82.368   1322
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.21 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 21.87 %
    Favored  : 73.20 %
  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:  0.16 (0.25), residues: 1152
  helix:  1.09 (0.20), residues: 724
  sheet: -0.95 (0.65), residues: 58
  loop : -1.70 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 316 
 TYR   0.011   0.001   TYR A 268 
 PHE   0.012   0.001   PHE B 291 
 TRP   0.005   0.001   TRP B 164 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9168)
  covalent geometry    : angle       0.64452 (12426)
  hydrogen bonds       : bond        0.04841 (  540)
  hydrogen bonds       : angle       4.49991 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 114
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8789 (t) cc_final: 0.8429 (p)
REVERT: A   80 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6355 (tt)
REVERT: A  386 LEU cc_start: 0.8858 (tp) cc_final: 0.8554 (tt)
REVERT: B   36 SER cc_start: 0.8761 (t) cc_final: 0.8419 (p)
REVERT: B  510 ASP cc_start: 0.6484 (p0) cc_final: 0.6280 (p0)
  outliers start: 48
  outliers final: 28
  residues processed: 157
  average time/residue: 0.0943
  time to fit residues: 20.8988
Evaluate side-chains
  135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  436 CYS
Chi-restraints excluded: chain B residue  577 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 52 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 58 optimal weight:    0.2980
   chunk 92 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0060
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.197877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.159188 restraints weight = 10530.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.157223 restraints weight = 11188.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.160034 restraints weight = 10109.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.160472 restraints weight = 7471.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.160402 restraints weight = 6930.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9168  Z= 0.144
  Angle     :  0.666  11.194  12426  Z= 0.329
  Chirality :  0.043   0.444   1486
  Planarity :  0.004   0.040   1546
  Dihedral  :  9.005  87.082   1322
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.12 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 23.51 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.25), residues: 1152
  helix:  1.19 (0.20), residues: 736
  sheet: -0.93 (0.65), residues: 58
  loop : -1.73 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 536 
 TYR   0.012   0.001   TYR B 268 
 PHE   0.017   0.001   PHE B 291 
 TRP   0.005   0.001   TRP A 164 
 HIS   0.003   0.000   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9168)
  covalent geometry    : angle       0.66574 (12426)
  hydrogen bonds       : bond        0.04826 (  540)
  hydrogen bonds       : angle       4.44604 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8832 (t) cc_final: 0.8378 (p)
REVERT: A  318 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8707 (mt)
REVERT: A  386 LEU cc_start: 0.8897 (tp) cc_final: 0.8567 (tt)
REVERT: B   36 SER cc_start: 0.8793 (t) cc_final: 0.8427 (p)
REVERT: B  295 MET cc_start: 0.8396 (tmm) cc_final: 0.8174 (tpp)
REVERT: B  318 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8706 (mt)
REVERT: B  386 LEU cc_start: 0.8944 (tp) cc_final: 0.8595 (tt)
REVERT: B  510 ASP cc_start: 0.6537 (p0) cc_final: 0.6212 (p0)
  outliers start: 38
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0931
  time to fit residues: 20.0859
Evaluate side-chains
  135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  436 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 73 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.195635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.157482 restraints weight = 10582.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.154436 restraints weight = 8638.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.155955 restraints weight = 8344.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.156389 restraints weight = 7458.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.156444 restraints weight = 6573.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9168  Z= 0.175
  Angle     :  0.669  12.097  12426  Z= 0.337
  Chirality :  0.043   0.196   1486
  Planarity :  0.004   0.039   1546
  Dihedral  :  9.011  84.897   1322
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.47 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 23.10 %
    Favored  : 72.07 %
  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:  0.16 (0.25), residues: 1152
  helix:  1.04 (0.19), residues: 750
  sheet: -1.80 (0.53), residues: 82
  loop : -1.52 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 399 
 TYR   0.012   0.001   TYR A 419 
 PHE   0.015   0.001   PHE A  75 
 TRP   0.006   0.001   TRP A 413 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9168)
  covalent geometry    : angle       0.66874 (12426)
  hydrogen bonds       : bond        0.04921 (  540)
  hydrogen bonds       : angle       4.45293 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 107
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8900 (t) cc_final: 0.8353 (p)
REVERT: A  318 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8715 (mt)
REVERT: A  386 LEU cc_start: 0.8951 (tp) cc_final: 0.8607 (tt)
REVERT: A  398 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6716 (mp)
REVERT: B   36 SER cc_start: 0.8898 (t) cc_final: 0.8434 (p)
REVERT: B  295 MET cc_start: 0.8513 (tmm) cc_final: 0.8301 (tpp)
REVERT: B  318 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8744 (mt)
REVERT: B  386 LEU cc_start: 0.8929 (tp) cc_final: 0.8562 (tt)
REVERT: B  510 ASP cc_start: 0.6570 (p0) cc_final: 0.6125 (p0)
  outliers start: 47
  outliers final: 32
  residues processed: 150
  average time/residue: 0.0922
  time to fit residues: 19.5197
Evaluate side-chains
  136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  436 CYS
Chi-restraints excluded: chain B residue  487 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 83 optimal weight:   20.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.196639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.158847 restraints weight = 10532.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.156875 restraints weight = 9069.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.157488 restraints weight = 8511.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157888 restraints weight = 7701.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.158218 restraints weight = 6828.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9168  Z= 0.161
  Angle     :  0.690  12.386  12426  Z= 0.340
  Chirality :  0.044   0.428   1486
  Planarity :  0.004   0.038   1546
  Dihedral  :  8.909  88.504   1322
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.12 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.95 %
    Favored  : 71.36 %
  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:  0.20 (0.25), residues: 1152
  helix:  1.07 (0.19), residues: 750
  sheet: -1.74 (0.53), residues: 82
  loop : -1.48 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 399 
 TYR   0.013   0.001   TYR A 419 
 PHE   0.014   0.001   PHE A 291 
 TRP   0.005   0.001   TRP B 164 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9168)
  covalent geometry    : angle       0.68983 (12426)
  hydrogen bonds       : bond        0.04873 (  540)
  hydrogen bonds       : angle       4.43085 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8800 (t) cc_final: 0.8391 (p)
REVERT: A  318 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8772 (mt)
REVERT: A  386 LEU cc_start: 0.8925 (tp) cc_final: 0.8589 (tt)
REVERT: A  510 ASP cc_start: 0.6644 (p0) cc_final: 0.6328 (p0)
REVERT: A  580 MET cc_start: 0.7615 (tpp) cc_final: 0.7023 (tpp)
REVERT: B   36 SER cc_start: 0.8855 (t) cc_final: 0.8414 (p)
REVERT: B  253 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8353 (mt)
REVERT: B  386 LEU cc_start: 0.8939 (tp) cc_final: 0.8580 (tt)
REVERT: B  510 ASP cc_start: 0.6631 (p0) cc_final: 0.6341 (p0)
  outliers start: 36
  outliers final: 32
  residues processed: 142
  average time/residue: 0.0989
  time to fit residues: 19.6820
Evaluate side-chains
  136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 102
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  436 CYS
Chi-restraints excluded: chain B residue  487 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 18 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.191999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.150854 restraints weight = 10534.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.151114 restraints weight = 9909.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.153326 restraints weight = 7940.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.153642 restraints weight = 6171.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.153721 restraints weight = 6116.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9168  Z= 0.169
  Angle     :  0.665  12.741  12426  Z= 0.333
  Chirality :  0.043   0.295   1486
  Planarity :  0.004   0.039   1546
  Dihedral  :  8.851  88.150   1322
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.12 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 24.13 %
    Favored  : 71.77 %
  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:  0.26 (0.25), residues: 1152
  helix:  1.12 (0.19), residues: 746
  sheet: -1.69 (0.54), residues: 82
  loop : -1.50 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 399 
 TYR   0.012   0.001   TYR A 419 
 PHE   0.012   0.001   PHE B  75 
 TRP   0.007   0.001   TRP A 413 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9168)
  covalent geometry    : angle       0.66472 (12426)
  hydrogen bonds       : bond        0.04879 (  540)
  hydrogen bonds       : angle       4.42576 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8848 (t) cc_final: 0.8350 (p)
REVERT: A  386 LEU cc_start: 0.8951 (tp) cc_final: 0.8633 (tt)
REVERT: A  398 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6769 (mp)
REVERT: A  454 MET cc_start: 0.7476 (mmm) cc_final: 0.7087 (mtm)
REVERT: A  510 ASP cc_start: 0.6618 (p0) cc_final: 0.6342 (p0)
REVERT: B   36 SER cc_start: 0.8842 (t) cc_final: 0.8385 (p)
REVERT: B  386 LEU cc_start: 0.8980 (tp) cc_final: 0.8593 (tt)
REVERT: B  510 ASP cc_start: 0.6587 (p0) cc_final: 0.6279 (p0)
REVERT: B  580 MET cc_start: 0.7799 (tpp) cc_final: 0.7239 (tpp)
  outliers start: 40
  outliers final: 33
  residues processed: 145
  average time/residue: 0.0940
  time to fit residues: 19.0799
Evaluate side-chains
  137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  436 CYS
Chi-restraints excluded: chain B residue  487 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 96 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 106 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 88 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.197101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155718 restraints weight = 10467.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.154543 restraints weight = 10791.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.156201 restraints weight = 9422.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.157042 restraints weight = 8153.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.157250 restraints weight = 7163.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9168  Z= 0.147
  Angle     :  0.651   9.414  12426  Z= 0.326
  Chirality :  0.042   0.192   1486
  Planarity :  0.004   0.038   1546
  Dihedral  :  8.679  88.753   1322
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.86 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.74 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.25), residues: 1152
  helix:  1.20 (0.20), residues: 744
  sheet: -1.54 (0.55), residues: 82
  loop : -1.48 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 389 
 TYR   0.012   0.001   TYR A 419 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.005   0.001   TRP A 104 
 HIS   0.002   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9168)
  covalent geometry    : angle       0.65116 (12426)
  hydrogen bonds       : bond        0.04647 (  540)
  hydrogen bonds       : angle       4.35206 ( 1572)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 SER cc_start: 0.8790 (t) cc_final: 0.8313 (p)
REVERT: A  259 MET cc_start: 0.7924 (mmp) cc_final: 0.7715 (mmm)
REVERT: A  386 LEU cc_start: 0.8907 (tp) cc_final: 0.8588 (tt)
REVERT: A  398 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6526 (mp)
REVERT: A  510 ASP cc_start: 0.6732 (p0) cc_final: 0.6408 (p0)
REVERT: B   36 SER cc_start: 0.8837 (t) cc_final: 0.8373 (p)
REVERT: B  386 LEU cc_start: 0.8949 (tp) cc_final: 0.8572 (tt)
REVERT: B  510 ASP cc_start: 0.6624 (p0) cc_final: 0.6321 (p0)
REVERT: B  519 GLN cc_start: 0.7957 (tp40) cc_final: 0.7723 (tp40)
REVERT: B  580 MET cc_start: 0.7832 (tpp) cc_final: 0.7282 (tpp)
  outliers start: 35
  outliers final: 31
  residues processed: 137
  average time/residue: 0.0901
  time to fit residues: 17.4759
Evaluate side-chains
  137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  324 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  398 ILE
Chi-restraints excluded: chain B residue  436 CYS
Chi-restraints excluded: chain B residue  487 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 110 optimal weight:    0.1980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 467 GLN
B 342 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.197638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.155242 restraints weight = 10440.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.155638 restraints weight = 10619.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.158212 restraints weight = 8514.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.158826 restraints weight = 6454.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.158807 restraints weight = 6308.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9168  Z= 0.144
  Angle     :  0.631  11.028  12426  Z= 0.318
  Chirality :  0.042   0.183   1486
  Planarity :  0.004   0.039   1546
  Dihedral  :  8.489  87.329   1322
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.74 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.25), residues: 1152
  helix:  1.26 (0.20), residues: 742
  sheet: -1.40 (0.56), residues: 82
  loop : -1.48 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.011   0.001   TYR A 419 
 PHE   0.009   0.001   PHE A 291 
 TRP   0.005   0.001   TRP A 104 
 HIS   0.002   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9168)
  covalent geometry    : angle       0.63138 (12426)
  hydrogen bonds       : bond        0.04498 (  540)
  hydrogen bonds       : angle       4.28115 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1419.80 seconds
wall clock time: 25 minutes 22.92 seconds (1522.92 seconds total)