Starting phenix.real_space_refine
on Wed Mar  4 02:10:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dnz_30791/03_2026/7dnz_30791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dnz_30791/03_2026/7dnz_30791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dnz_30791/03_2026/7dnz_30791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dnz_30791/03_2026/7dnz_30791.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dnz_30791/03_2026/7dnz_30791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dnz_30791/03_2026/7dnz_30791.map"
  }
  resolution = 3.6
  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=   0.003 sd=   0.046
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      38      5.16       5
     C    6256      2.51       5
     N    1634      2.21       5
     O    1742      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9671
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4669
          Classifications: {'peptide': 591}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 577}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 4669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4669
          Classifications: {'peptide': 591}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 577}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 145
          Unusual residues: {'GSH': 2, 'Y01': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 188
          Unusual residues: {'GSH': 2, 'HEM': 1, 'Y01': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 2.61, per 1000 atoms: 0.27
  Number of scatterers: 9671
  At special positions: 0
  Unit cell: (80.51, 98.77, 137.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      38     16.00
     O    1742      8.00
     N    1634      7.00
     C    6256      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: 0.91
  Conformation dependent library (CDL) restraints added in 577.0 milliseconds
  

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2176

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      70.7% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 239 through 254
      removed outlier: 3.610A  pdb=" N   GLY A 243 " --> pdb=" O   TRP A 239 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ARG A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS A 245 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TRP A 254 " --> pdb=" O   SER A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 295
      removed outlier: 4.006A  pdb=" N   VAL A 280 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
      removed outlier: 3.656A  pdb=" N   GLU A 295 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 316
      removed outlier: 3.637A  pdb=" N   LEU A 302 " --> pdb=" O   PRO A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 355
      removed outlier: 3.512A  pdb=" N   ARG A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ARG A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   VAL A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN A 338 " --> pdb=" O   TRP A 334 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN A 339 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.946A  pdb=" N   HIS A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 390
      removed outlier: 3.806A  pdb=" N   VAL A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LEU A 370 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ARG A 371 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 409
    Processing helix  chain 'A' and resid 410 through 459
      removed outlier: 3.700A  pdb=" N   GLY A 414 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   LYS A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   PHE A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 467
      removed outlier: 3.513A  pdb=" N   ASN A 467 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 522
      removed outlier: 4.276A  pdb=" N   LYS A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 545
      removed outlier: 4.327A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      Proline residue:  A 543  - end of helix
    Processing helix  chain 'A' and resid 546 through 570
      removed outlier: 3.699A  pdb=" N   TYR A 550 " --> pdb=" O   TRP A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 637
    Processing helix  chain 'A' and resid 658 through 665
    Processing helix  chain 'A' and resid 680 through 685
    Processing helix  chain 'A' and resid 692 through 704
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 728 through 744
    Processing helix  chain 'A' and resid 758 through 773
    Processing helix  chain 'A' and resid 784 through 790
    Processing helix  chain 'A' and resid 807 through 815
    Processing helix  chain 'A' and resid 816 through 825
      removed outlier: 3.672A  pdb=" N   ASP A 820 " --> pdb=" O   GLY A 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 254
      removed outlier: 3.610A  pdb=" N   GLY B 243 " --> pdb=" O   TRP B 239 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ARG B 244 " --> pdb=" O   ARG B 240 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS B 245 " --> pdb=" O   ASP B 241 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TRP B 254 " --> pdb=" O   SER B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 295
      removed outlier: 4.006A  pdb=" N   VAL B 280 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 3.656A  pdb=" N   GLU B 295 " --> pdb=" O   ASN B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 316
      removed outlier: 3.638A  pdb=" N   LEU B 302 " --> pdb=" O   PRO B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 355
      removed outlier: 4.887A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   VAL B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN B 338 " --> pdb=" O   TRP B 334 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN B 339 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 364
      removed outlier: 3.946A  pdb=" N   HIS B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 390
      removed outlier: 3.805A  pdb=" N   VAL B 369 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU B 370 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ARG B 371 " --> pdb=" O   GLY B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 409
    Processing helix  chain 'B' and resid 410 through 459
      removed outlier: 3.700A  pdb=" N   GLY B 414 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   LYS B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   PHE B 438 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 467
      removed outlier: 3.513A  pdb=" N   ASN B 467 " --> pdb=" O   VAL B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 522
      removed outlier: 4.276A  pdb=" N   LYS B 489 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 545
      removed outlier: 4.327A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      Proline residue:  B 543  - end of helix
    Processing helix  chain 'B' and resid 546 through 570
      removed outlier: 3.699A  pdb=" N   TYR B 550 " --> pdb=" O   TRP B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 637
    Processing helix  chain 'B' and resid 658 through 665
    Processing helix  chain 'B' and resid 680 through 685
    Processing helix  chain 'B' and resid 692 through 704
    Processing helix  chain 'B' and resid 705 through 712
    Processing helix  chain 'B' and resid 728 through 744
    Processing helix  chain 'B' and resid 758 through 773
    Processing helix  chain 'B' and resid 784 through 790
    Processing helix  chain 'B' and resid 807 through 815
    Processing helix  chain 'B' and resid 816 through 825
      removed outlier: 3.671A  pdb=" N   ASP B 820 " --> pdb=" O   GLY B 816 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 596
      removed outlier: 3.524A  pdb=" N   GLU A 591 " --> pdb=" O   ARG A 648 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG A 648 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU A 593 " --> pdb=" O   CYS A 646 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS A 646 " --> pdb=" O   GLU A 593 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL A 595 " --> pdb=" O   SER A 644 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   SER A 644 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 618 through 621
      removed outlier: 3.652A  pdb=" N   ILE A 779 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 781 " --> pdb=" O   LEU A 750 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 679
    Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 798
      removed outlier: 3.839A  pdb=" N   GLY A 806 " --> pdb=" O   ILE A 794 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 804 " --> pdb=" O   VAL A 796 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LYS A 798 " --> pdb=" O   ILE A 802 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ILE A 802 " --> pdb=" O   LYS A 798 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 590 through 596
      removed outlier: 3.525A  pdb=" N   GLU B 591 " --> pdb=" O   ARG B 648 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG B 648 " --> pdb=" O   GLU B 591 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU B 593 " --> pdb=" O   CYS B 646 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   CYS B 646 " --> pdb=" O   GLU B 593 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   VAL B 595 " --> pdb=" O   SER B 644 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   SER B 644 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 618 through 621
      removed outlier: 3.652A  pdb=" N   ILE B 779 " --> pdb=" O   ILE B 748 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL B 781 " --> pdb=" O   LEU B 750 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 678 through 679
    Processing sheet with id=AA8, first strand: chain 'B' and resid 794 through 798
      removed outlier: 3.839A  pdb=" N   GLY B 806 " --> pdb=" O   ILE B 794 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU B 804 " --> pdb=" O   VAL B 796 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LYS B 798 " --> pdb=" O   ILE B 802 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ILE B 802 " --> pdb=" O   LYS B 798 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1857 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: 1.67

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.20 -     1.38: 3768
        1.38 -     1.56: 6038
        1.56 -     1.74: 4
        1.74 -     1.92: 61
        1.92 -     2.10: 3
  Bond restraints: 9874
  Sorted by residual:
  bond pdb=" C3C HEM B 901 "
       pdb=" CAC HEM B 901 "
    ideal  model  delta    sigma   weight residual
    1.544  1.471  0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C3B HEM B 901 "
       pdb=" CAB HEM B 901 "
    ideal  model  delta    sigma   weight residual
    1.544  1.475  0.069 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C1  GSH B 903 "
       pdb=" O12 GSH B 903 "
    ideal  model  delta    sigma   weight residual
    1.307  1.244  0.063 1.90e-02 2.77e+03 1.09e+01
  bond pdb=" C1  GSH A 902 "
       pdb=" O12 GSH A 902 "
    ideal  model  delta    sigma   weight residual
    1.307  1.245  0.062 1.90e-02 2.77e+03 1.07e+01
  bond pdb=" C1  GSH B 902 "
       pdb=" O11 GSH B 902 "
    ideal  model  delta    sigma   weight residual
    1.213  1.246 -0.033 1.00e-02 1.00e+04 1.06e+01
  ... (remaining 9869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 12524
        1.99 -     3.97: 724
        3.97 -     5.96: 132
        5.96 -     7.94: 34
        7.94 -     9.93: 18
  Bond angle restraints: 13432
  Sorted by residual:
  angle pdb=" C   PHE B 325 "
        pdb=" N   VAL B 326 "
        pdb=" CA  VAL B 326 "
      ideal   model   delta    sigma   weight residual
     122.63  113.76    8.87 1.19e+00 7.06e-01 5.56e+01
  angle pdb=" C   THR A 320 "
        pdb=" CA  THR A 320 "
        pdb=" CB  THR A 320 "
      ideal   model   delta    sigma   weight residual
     109.72  119.03   -9.31 1.66e+00 3.63e-01 3.15e+01
  angle pdb=" N   GLY A 318 "
        pdb=" CA  GLY A 318 "
        pdb=" C   GLY A 318 "
      ideal   model   delta    sigma   weight residual
     112.73  106.03    6.70 1.20e+00 6.94e-01 3.12e+01
  angle pdb=" N   VAL A 280 "
        pdb=" CA  VAL A 280 "
        pdb=" C   VAL A 280 "
      ideal   model   delta    sigma   weight residual
     112.96  108.41    4.55 1.00e+00 1.00e+00 2.07e+01
  angle pdb=" N   SER B 322 "
        pdb=" CA  SER B 322 "
        pdb=" C   SER B 322 "
      ideal   model   delta    sigma   weight residual
     108.24  102.24    6.00 1.32e+00 5.74e-01 2.07e+01
  ... (remaining 13427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5390
       17.94 -    35.88: 578
       35.88 -    53.82: 111
       53.82 -    71.76: 30
       71.76 -    89.69: 11
  Dihedral angle restraints: 6120
    sinusoidal: 2720
      harmonic: 3400
  Sorted by residual:
  dihedral pdb=" C2B HEM B 901 "
           pdb=" C3B HEM B 901 "
           pdb=" CAB HEM B 901 "
           pdb=" CBB HEM B 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.87  -71.87     2      1.00e+01 1.00e-02 4.34e+01
  dihedral pdb=" C2C HEM B 901 "
           pdb=" C3C HEM B 901 "
           pdb=" CAC HEM B 901 "
           pdb=" CBC HEM B 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -65.50   65.50     2      1.00e+01 1.00e-02 3.97e+01
  dihedral pdb=" C   THR A 320 "
           pdb=" N   THR A 320 "
           pdb=" CA  THR A 320 "
           pdb=" CB  THR A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.24   14.24     0      2.50e+00 1.60e-01 3.24e+01
  ... (remaining 6117 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1360
       0.094 -    0.187: 178
       0.187 -    0.281: 9
       0.281 -    0.375: 0
       0.375 -    0.468: 1
  Chirality restraints: 1548
  Sorted by residual:
  chirality pdb=" CA  THR A 320 "
            pdb=" N   THR A 320 "
            pdb=" C   THR A 320 "
            pdb=" CB  THR A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.06    0.47 2.00e-01 2.50e+01 5.48e+00
  chirality pdb=" CA  PHE B 408 "
            pdb=" N   PHE B 408 "
            pdb=" C   PHE B 408 "
            pdb=" CB  PHE B 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  THR B 320 "
            pdb=" N   THR B 320 "
            pdb=" C   THR B 320 "
            pdb=" CB  THR B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.57e+00
  ... (remaining 1545 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG1 GSH A 901 "    0.162 2.00e-02 2.50e+03   1.94e-01 4.71e+02
        pdb=" CD1 GSH A 901 "   -0.064 2.00e-02 2.50e+03
        pdb=" OE1 GSH A 901 "   -0.009 2.00e-02 2.50e+03
        pdb=" CA2 GSH A 901 "    0.233 2.00e-02 2.50e+03
        pdb=" N2  GSH A 901 "   -0.322 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG1 GSH B 902 "    0.136 2.00e-02 2.50e+03   1.56e-01 3.05e+02
        pdb=" CD1 GSH B 902 "   -0.051 2.00e-02 2.50e+03
        pdb=" OE1 GSH B 902 "   -0.018 2.00e-02 2.50e+03
        pdb=" CA2 GSH B 902 "    0.188 2.00e-02 2.50e+03
        pdb=" N2  GSH B 902 "   -0.255 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  GSH B 902 "   -0.043 2.00e-02 2.50e+03   1.26e-01 1.97e+02
        pdb=" CA2 GSH B 902 "    0.113 2.00e-02 2.50e+03
        pdb=" CA3 GSH B 902 "    0.153 2.00e-02 2.50e+03
        pdb=" N3  GSH B 902 "   -0.201 2.00e-02 2.50e+03
        pdb=" O2  GSH B 902 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2824
        2.82 -     3.34: 9776
        3.34 -     3.86: 15815
        3.86 -     4.38: 16675
        4.38 -     4.90: 28224
  Nonbonded interactions: 73314
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS B 808 "
            pdb=" OH  TYR B 818 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND1 HIS A 808 "
            pdb=" OH  TYR A 818 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" NH1 ARG B 638 "
            pdb=" O   ILE B 654 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" NH1 ARG A 638 "
            pdb=" O   ILE A 654 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OH  TYR A 424 "
            pdb=" OE1 GLN A 501 "
     model   vdw
     2.312 3.040
  ... (remaining 73309 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 236 through 826 or resid 902 or resid 904 through 905))
  selection = (chain 'B' and (resid 236 through 826 or resid 902 or resid 904 through 905))
}

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=0.50 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:             2.120
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.290
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
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      :  0.009   0.219   9874  Z= 0.442
  Angle     :  1.121   9.926  13432  Z= 0.636
  Chirality :  0.061   0.468   1548
  Planarity :  0.010   0.194   1668
  Dihedral  : 15.293  89.694   3944
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.10 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.09 %
  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: -0.69 (0.23), residues: 1178
  helix:  0.53 (0.18), residues: 780
  sheet: -2.29 (0.65), residues: 50
  loop : -2.39 (0.28), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 663 
 TYR   0.032   0.003   TYR B 466 
 PHE   0.050   0.004   PHE B 460 
 TRP   0.008   0.001   TRP A 304 
 HIS   0.007   0.002   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00942 ( 9874)
  covalent geometry    : angle       1.12080 (13432)
  hydrogen bonds       : bond        0.14736 (  625)
  hydrogen bonds       : angle       5.57330 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8517 (tm-30)
REVERT: A  408 PHE cc_start: 0.7597 (m-80) cc_final: 0.7083 (m-10)
REVERT: A  452 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7864 (tpp80)
REVERT: A  614 MET cc_start: 0.8929 (mpp) cc_final: 0.8299 (mpp)
REVERT: A  748 ILE cc_start: 0.8701 (mt) cc_final: 0.8475 (mt)
REVERT: B  275 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8453 (tm-30)
REVERT: B  408 PHE cc_start: 0.7738 (m-80) cc_final: 0.7112 (m-10)
REVERT: B  452 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7951 (tpp80)
REVERT: B  614 MET cc_start: 0.8889 (mpp) cc_final: 0.8231 (mpp)
REVERT: B  748 ILE cc_start: 0.8667 (mt) cc_final: 0.8430 (mt)
  outliers start: 6
  outliers final: 3
  residues processed: 147
  average time/residue: 0.0786
  time to fit residues: 17.8305
Evaluate side-chains
  95 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  455 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    0.0170
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.9622

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 316 GLN
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
A 539 GLN
A 557 ASN
B 279 ASN
B 316 GLN
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 HIS
B 539 GLN
B 557 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.147633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.103008 restraints weight = 16406.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.106261 restraints weight = 7299.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.108454 restraints weight = 4385.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.109743 restraints weight = 3183.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.110645 restraints weight = 2640.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3661 r_free = 0.3661    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9874  Z= 0.151
  Angle     :  0.597   9.096  13432  Z= 0.304
  Chirality :  0.039   0.138   1548
  Planarity :  0.004   0.039   1668
  Dihedral  : 10.105  88.675   1819
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.24 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.50 (0.24), residues: 1178
  helix:  1.40 (0.18), residues: 806
  sheet: -0.07 (0.73), residues: 30
  loop : -2.33 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 685 
 TYR   0.013   0.001   TYR B 466 
 PHE   0.015   0.001   PHE A 519 
 TRP   0.007   0.001   TRP A 334 
 HIS   0.003   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9874)
  covalent geometry    : angle       0.59745 (13432)
  hydrogen bonds       : bond        0.06683 (  625)
  hydrogen bonds       : angle       4.44311 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8387 (tm-30)
REVERT: A  407 MET cc_start: 0.8201 (tmm) cc_final: 0.7927 (tmm)
REVERT: A  539 GLN cc_start: 0.8364 (tt0) cc_final: 0.7865 (tt0)
REVERT: A  614 MET cc_start: 0.8962 (mpp) cc_final: 0.8276 (mpp)
REVERT: A  666 ILE cc_start: 0.8840 (tp) cc_final: 0.8610 (tp)
REVERT: A  671 GLN cc_start: 0.7292 (tp-100) cc_final: 0.6762 (tp-100)
REVERT: A  748 ILE cc_start: 0.8367 (mt) cc_final: 0.8148 (mt)
REVERT: A  751 ASP cc_start: 0.6633 (t0) cc_final: 0.6424 (t0)
REVERT: A  821 MET cc_start: 0.7983 (tmm) cc_final: 0.7771 (tmm)
REVERT: B  275 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8372 (tm-30)
REVERT: B  407 MET cc_start: 0.8108 (tmm) cc_final: 0.7862 (tmm)
REVERT: B  614 MET cc_start: 0.8972 (mpp) cc_final: 0.8307 (mpp)
REVERT: B  671 GLN cc_start: 0.7273 (tp-100) cc_final: 0.6800 (tp-100)
REVERT: B  748 ILE cc_start: 0.8424 (mt) cc_final: 0.8199 (mt)
  outliers start: 22
  outliers final: 19
  residues processed: 134
  average time/residue: 0.0762
  time to fit residues: 15.9196
Evaluate side-chains
  122 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  442 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  725 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0370
   chunk 33 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 77 optimal weight:    4.9990
   chunk 105 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    2.4066

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.143951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.099095 restraints weight = 16603.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.102107 restraints weight = 7515.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.104180 restraints weight = 4572.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.105482 restraints weight = 3332.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.106185 restraints weight = 2755.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   9874  Z= 0.204
  Angle     :  0.635   7.826  13432  Z= 0.317
  Chirality :  0.040   0.156   1548
  Planarity :  0.003   0.035   1668
  Dihedral  :  9.318  76.048   1819
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.16 %
    Favored  : 80.52 %
  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:  0.94 (0.25), residues: 1178
  helix:  1.76 (0.19), residues: 806
  sheet:  0.01 (0.63), residues: 34
  loop : -2.22 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 330 
 TYR   0.013   0.001   TYR A 466 
 PHE   0.015   0.001   PHE B 408 
 TRP   0.011   0.001   TRP A 334 
 HIS   0.004   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 9874)
  covalent geometry    : angle       0.63511 (13432)
  hydrogen bonds       : bond        0.06638 (  625)
  hydrogen bonds       : angle       4.37867 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: A  442 MET cc_start: 0.8634 (ttt) cc_final: 0.8398 (ttm)
REVERT: A  614 MET cc_start: 0.8898 (mpp) cc_final: 0.8217 (mpp)
REVERT: A  637 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8340 (t80)
REVERT: A  671 GLN cc_start: 0.7439 (tp-100) cc_final: 0.6827 (tp-100)
REVERT: A  748 ILE cc_start: 0.8497 (mt) cc_final: 0.8253 (mt)
REVERT: A  750 LEU cc_start: 0.8818 (tt) cc_final: 0.8556 (tt)
REVERT: B  275 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: B  407 MET cc_start: 0.8386 (tmm) cc_final: 0.8111 (tmm)
REVERT: B  409 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8547 (m-10)
REVERT: B  614 MET cc_start: 0.8946 (mpp) cc_final: 0.8283 (mpp)
REVERT: B  637 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8425 (t80)
REVERT: B  705 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6641 (mp)
REVERT: B  748 ILE cc_start: 0.8460 (mt) cc_final: 0.8217 (mt)
  outliers start: 33
  outliers final: 20
  residues processed: 121
  average time/residue: 0.0679
  time to fit residues: 13.3740
Evaluate side-chains
  111 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  818 TYR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0270
   chunk 17 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 52 optimal weight:   30.0000
   chunk 103 optimal weight:    7.9990
   chunk 2 optimal weight:    0.4980
   chunk 74 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.8840

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

Flipped N/Q/H residues before XYZ refinement:
A 354 HIS
B 354 HIS
B 557 ASN
B 652 GLN
B 671 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.146641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.101267 restraints weight = 16647.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.104517 restraints weight = 7384.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.106667 restraints weight = 4435.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.108035 restraints weight = 3239.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.108752 restraints weight = 2691.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9874  Z= 0.128
  Angle     :  0.559   9.891  13432  Z= 0.272
  Chirality :  0.037   0.150   1548
  Planarity :  0.003   0.029   1668
  Dihedral  :  8.312  67.603   1818
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.67 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.25), residues: 1178
  helix:  2.04 (0.19), residues: 810
  sheet:  0.44 (0.70), residues: 34
  loop : -2.17 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 330 
 TYR   0.009   0.001   TYR B 465 
 PHE   0.010   0.001   PHE A 389 
 TRP   0.007   0.001   TRP B 334 
 HIS   0.003   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9874)
  covalent geometry    : angle       0.55916 (13432)
  hydrogen bonds       : bond        0.05574 (  625)
  hydrogen bonds       : angle       4.00690 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: A  614 MET cc_start: 0.8884 (mpp) cc_final: 0.8170 (mpp)
REVERT: A  671 GLN cc_start: 0.7356 (tp-100) cc_final: 0.7118 (tp-100)
REVERT: A  705 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6098 (mp)
REVERT: A  748 ILE cc_start: 0.8326 (mt) cc_final: 0.8120 (mt)
REVERT: A  750 LEU cc_start: 0.8645 (tt) cc_final: 0.8351 (tt)
REVERT: B  275 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: B  315 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8479 (mp)
REVERT: B  389 PHE cc_start: 0.9004 (m-10) cc_final: 0.8746 (m-10)
REVERT: B  614 MET cc_start: 0.8915 (mpp) cc_final: 0.8215 (mpp)
REVERT: B  637 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8357 (t80)
REVERT: B  671 GLN cc_start: 0.7195 (tp-100) cc_final: 0.6957 (tp40)
REVERT: B  705 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6776 (mp)
REVERT: B  748 ILE cc_start: 0.8361 (mt) cc_final: 0.8155 (mt)
  outliers start: 30
  outliers final: 20
  residues processed: 139
  average time/residue: 0.0635
  time to fit residues: 14.5785
Evaluate side-chains
  123 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 354 HIS
B 354 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.148969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.103764 restraints weight = 16561.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.106985 restraints weight = 7407.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.109124 restraints weight = 4471.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.110483 restraints weight = 3277.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.111195 restraints weight = 2725.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9874  Z= 0.125
  Angle     :  0.579   8.962  13432  Z= 0.276
  Chirality :  0.037   0.147   1548
  Planarity :  0.003   0.029   1668
  Dihedral  :  7.942  70.424   1818
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.68 %
    Favored  : 77.11 %
  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:  1.51 (0.25), residues: 1178
  helix:  2.16 (0.19), residues: 812
  sheet:  0.69 (0.75), residues: 34
  loop : -2.08 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 344 
 TYR   0.010   0.001   TYR A 466 
 PHE   0.014   0.001   PHE A 460 
 TRP   0.007   0.001   TRP B 334 
 HIS   0.008   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9874)
  covalent geometry    : angle       0.57884 (13432)
  hydrogen bonds       : bond        0.05371 (  625)
  hydrogen bonds       : angle       3.89386 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8368 (tm-30)
REVERT: A  315 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8529 (mp)
REVERT: A  338 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8300 (tm-30)
REVERT: A  539 GLN cc_start: 0.8388 (tt0) cc_final: 0.7946 (tt0)
REVERT: A  553 MET cc_start: 0.8470 (mtm) cc_final: 0.8205 (mtp)
REVERT: A  637 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8205 (t80)
REVERT: A  705 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6191 (mp)
REVERT: A  748 ILE cc_start: 0.8276 (mt) cc_final: 0.8069 (mt)
REVERT: A  750 LEU cc_start: 0.8662 (tt) cc_final: 0.8342 (tt)
REVERT: B  275 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: B  389 PHE cc_start: 0.8987 (m-10) cc_final: 0.8734 (m-10)
REVERT: B  539 GLN cc_start: 0.8373 (tt0) cc_final: 0.8150 (tt0)
REVERT: B  705 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6752 (mp)
REVERT: B  748 ILE cc_start: 0.8317 (mt) cc_final: 0.8108 (mt)
  outliers start: 32
  outliers final: 22
  residues processed: 135
  average time/residue: 0.0645
  time to fit residues: 14.3060
Evaluate side-chains
  128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 113 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 102 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 107 optimal weight:    0.2980
   chunk 41 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0370
   overall best weight:    0.6060

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

Flipped N/Q/H residues before XYZ refinement:
A 354 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.150254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.104993 restraints weight = 16497.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.108321 restraints weight = 7059.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.110545 restraints weight = 4166.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.111956 restraints weight = 3008.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.112680 restraints weight = 2487.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3721 r_free = 0.3721    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3721 r_free = 0.3721    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9874  Z= 0.118
  Angle     :  0.578   9.044  13432  Z= 0.273
  Chirality :  0.037   0.146   1548
  Planarity :  0.003   0.024   1668
  Dihedral  :  7.714  74.576   1818
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.88 %
    Favored  : 76.10 %
  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:  1.63 (0.25), residues: 1178
  helix:  2.25 (0.19), residues: 812
  sheet:  1.04 (0.77), residues: 34
  loop : -2.04 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 330 
 TYR   0.013   0.001   TYR A 465 
 PHE   0.008   0.001   PHE B 533 
 TRP   0.007   0.000   TRP B 334 
 HIS   0.013   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9874)
  covalent geometry    : angle       0.57831 (13432)
  hydrogen bonds       : bond        0.05045 (  625)
  hydrogen bonds       : angle       3.79447 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8318 (tm-30)
REVERT: A  279 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8627 (t0)
REVERT: A  315 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8410 (mp)
REVERT: A  338 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: A  539 GLN cc_start: 0.8375 (tt0) cc_final: 0.8119 (tt0)
REVERT: A  637 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8126 (t80)
REVERT: A  671 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6887 (tp-100)
REVERT: A  705 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6235 (mp)
REVERT: A  750 LEU cc_start: 0.8676 (tt) cc_final: 0.8321 (tt)
REVERT: B  275 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: B  315 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8380 (mp)
REVERT: B  389 PHE cc_start: 0.8953 (m-10) cc_final: 0.8678 (m-10)
REVERT: B  539 GLN cc_start: 0.8371 (tt0) cc_final: 0.7867 (tt0)
REVERT: B  637 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8204 (t80)
REVERT: B  705 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6851 (mp)
  outliers start: 30
  outliers final: 18
  residues processed: 131
  average time/residue: 0.0660
  time to fit residues: 14.1554
Evaluate side-chains
  133 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 ASN
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.148650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.103759 restraints weight = 16622.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.106967 restraints weight = 7410.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.109093 restraints weight = 4454.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.110415 restraints weight = 3262.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.111258 restraints weight = 2719.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9874  Z= 0.125
  Angle     :  0.597   9.848  13432  Z= 0.279
  Chirality :  0.037   0.162   1548
  Planarity :  0.003   0.023   1668
  Dihedral  :  7.629  78.656   1818
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 20.98 %
    Favored  : 74.90 %
  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:  1.78 (0.25), residues: 1178
  helix:  2.34 (0.19), residues: 812
  sheet:  1.16 (0.79), residues: 34
  loop : -1.93 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 634 
 TYR   0.012   0.001   TYR A 466 
 PHE   0.043   0.001   PHE A 460 
 TRP   0.007   0.000   TRP B 334 
 HIS   0.004   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9874)
  covalent geometry    : angle       0.59666 (13432)
  hydrogen bonds       : bond        0.05099 (  625)
  hydrogen bonds       : angle       3.74207 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 108
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: A  279 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8593 (t0)
REVERT: A  539 GLN cc_start: 0.8387 (tt0) cc_final: 0.8140 (tt0)
REVERT: A  637 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8104 (t80)
REVERT: A  671 GLN cc_start: 0.7118 (tp-100) cc_final: 0.6905 (tp-100)
REVERT: A  705 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6220 (mp)
REVERT: A  750 LEU cc_start: 0.8717 (tt) cc_final: 0.8348 (tt)
REVERT: B  275 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8449 (tm-30)
REVERT: B  389 PHE cc_start: 0.8999 (m-10) cc_final: 0.8748 (m-10)
REVERT: B  465 TYR cc_start: 0.8952 (m-80) cc_final: 0.8677 (m-80)
REVERT: B  539 GLN cc_start: 0.8379 (tt0) cc_final: 0.7885 (tt0)
REVERT: B  637 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8230 (t80)
REVERT: B  705 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6780 (mp)
  outliers start: 41
  outliers final: 24
  residues processed: 134
  average time/residue: 0.0677
  time to fit residues: 14.8162
Evaluate side-chains
  134 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  279 ASN
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
B 279 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.145257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.099976 restraints weight = 16533.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.103055 restraints weight = 7514.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.105087 restraints weight = 4566.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.106409 restraints weight = 3352.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.107038 restraints weight = 2791.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9874  Z= 0.194
  Angle     :  0.691  13.605  13432  Z= 0.320
  Chirality :  0.039   0.167   1548
  Planarity :  0.003   0.023   1668
  Dihedral  :  7.904  78.499   1818
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 21.79 %
    Favored  : 74.50 %
  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:  1.68 (0.25), residues: 1178
  helix:  2.35 (0.19), residues: 800
  sheet:  0.86 (0.79), residues: 34
  loop : -2.02 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 638 
 TYR   0.011   0.001   TYR A 476 
 PHE   0.030   0.002   PHE A 460 
 TRP   0.007   0.001   TRP B 334 
 HIS   0.005   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 9874)
  covalent geometry    : angle       0.69111 (13432)
  hydrogen bonds       : bond        0.06019 (  625)
  hydrogen bonds       : angle       4.00645 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8337 (tm-30)
REVERT: A  279 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8585 (t0)
REVERT: A  539 GLN cc_start: 0.8445 (tt0) cc_final: 0.8044 (tt0)
REVERT: A  637 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8280 (t80)
REVERT: A  671 GLN cc_start: 0.7103 (tp-100) cc_final: 0.6871 (tp-100)
REVERT: A  705 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6191 (mp)
REVERT: A  750 LEU cc_start: 0.8843 (tt) cc_final: 0.8500 (tt)
REVERT: B  275 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: B  279 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8540 (t0)
REVERT: B  315 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (tp)
REVERT: B  539 GLN cc_start: 0.8395 (tt0) cc_final: 0.8019 (tt0)
REVERT: B  637 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8383 (t80)
REVERT: B  705 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6534 (mp)
  outliers start: 37
  outliers final: 25
  residues processed: 127
  average time/residue: 0.0671
  time to fit residues: 14.0201
Evaluate side-chains
  129 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  279 ASN
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0980
   chunk 64 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.146628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.101978 restraints weight = 16524.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.105164 restraints weight = 7311.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.107286 restraints weight = 4375.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.108509 restraints weight = 3182.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.109434 restraints weight = 2651.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3710
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3710 r_free = 0.3710    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3710 r_free = 0.3710    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3710
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9874  Z= 0.132
  Angle     :  0.640  12.797  13432  Z= 0.295
  Chirality :  0.038   0.173   1548
  Planarity :  0.003   0.023   1668
  Dihedral  :  7.777  78.881   1818
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.89 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.25), residues: 1178
  helix:  2.41 (0.19), residues: 800
  sheet:  0.87 (0.82), residues: 34
  loop : -1.95 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 638 
 TYR   0.015   0.001   TYR A 476 
 PHE   0.029   0.001   PHE A 460 
 TRP   0.006   0.001   TRP B 334 
 HIS   0.004   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9874)
  covalent geometry    : angle       0.63966 (13432)
  hydrogen bonds       : bond        0.05524 (  625)
  hydrogen bonds       : angle       3.84784 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: A  539 GLN cc_start: 0.8367 (tt0) cc_final: 0.8144 (tt0)
REVERT: A  637 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8159 (t80)
REVERT: A  671 GLN cc_start: 0.7035 (tp-100) cc_final: 0.6833 (tp-100)
REVERT: A  705 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6327 (mp)
REVERT: A  750 LEU cc_start: 0.8804 (tt) cc_final: 0.8453 (tt)
REVERT: B  275 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: B  637 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8287 (t80)
REVERT: B  705 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6672 (mp)
  outliers start: 37
  outliers final: 25
  residues processed: 128
  average time/residue: 0.0677
  time to fit residues: 14.0113
Evaluate side-chains
  129 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  481 ILE
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0870
   chunk 102 optimal weight:    0.7980
   chunk 116 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 46 optimal weight:    0.2980
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
A 557 ASN
** A 706 HIS ** 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 = 0.4222 r_free = 0.4222 target = 0.147907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.103609 restraints weight = 16413.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.106762 restraints weight = 7209.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.108894 restraints weight = 4294.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.110174 restraints weight = 3111.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111064 restraints weight = 2584.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9874  Z= 0.126
  Angle     :  0.640  11.400  13432  Z= 0.297
  Chirality :  0.038   0.174   1548
  Planarity :  0.003   0.024   1668
  Dihedral  :  7.711  80.703   1818
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 24.00 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.25), residues: 1178
  helix:  2.33 (0.19), residues: 814
  sheet:  0.86 (0.83), residues: 34
  loop : -1.76 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 359 
 TYR   0.015   0.001   TYR A 476 
 PHE   0.027   0.001   PHE A 460 
 TRP   0.006   0.001   TRP B 334 
 HIS   0.006   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9874)
  covalent geometry    : angle       0.64001 (13432)
  hydrogen bonds       : bond        0.05196 (  625)
  hydrogen bonds       : angle       3.79556 ( 1857)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8410 (tm-30)
REVERT: A  539 GLN cc_start: 0.8379 (tt0) cc_final: 0.7897 (tt0)
REVERT: A  637 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8166 (t80)
REVERT: A  671 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6771 (tp-100)
REVERT: A  705 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6425 (mp)
REVERT: A  750 LEU cc_start: 0.8791 (tt) cc_final: 0.8422 (tt)
REVERT: B  275 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: B  389 PHE cc_start: 0.9030 (m-10) cc_final: 0.8722 (m-10)
REVERT: B  522 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8614 (tt0)
REVERT: B  637 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8246 (t80)
REVERT: B  705 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6722 (mp)
  outliers start: 30
  outliers final: 25
  residues processed: 130
  average time/residue: 0.0680
  time to fit residues: 14.4319
Evaluate side-chains
  137 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  455 ASP
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  481 ILE
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  522 GLU
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  637 PHE
Chi-restraints excluded: chain B residue  668 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 2 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0670
   chunk 81 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 64 optimal weight:    0.7980
   chunk 112 optimal weight:    7.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.149884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.105680 restraints weight = 16435.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.108850 restraints weight = 7329.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.110986 restraints weight = 4405.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.112229 restraints weight = 3199.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.113141 restraints weight = 2667.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9874  Z= 0.126
  Angle     :  0.644  10.657  13432  Z= 0.298
  Chirality :  0.038   0.234   1548
  Planarity :  0.003   0.025   1668
  Dihedral  :  7.666  82.337   1818
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 24.10 %
    Favored  : 72.49 %
  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:  1.90 (0.26), residues: 1178
  helix:  2.39 (0.19), residues: 814
  sheet:  0.92 (0.83), residues: 34
  loop : -1.75 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 452 
 TYR   0.013   0.001   TYR A 476 
 PHE   0.026   0.001   PHE A 460 
 TRP   0.007   0.001   TRP B 334 
 HIS   0.009   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9874)
  covalent geometry    : angle       0.64373 (13432)
  hydrogen bonds       : bond        0.05039 (  625)
  hydrogen bonds       : angle       3.74324 ( 1857)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1782.35 seconds
wall clock time: 31 minutes 30.11 seconds (1890.11 seconds total)