Starting phenix.real_space_refine
on Tue Mar  3 15:18:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxf_32877/03_2026/7wxf_32877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxf_32877/03_2026/7wxf_32877.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/7wxf_32877/03_2026/7wxf_32877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxf_32877/03_2026/7wxf_32877.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxf_32877/03_2026/7wxf_32877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxf_32877/03_2026/7wxf_32877.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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    4054      2.51       5
     N    1172      2.21       5
     O    1238      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 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: 6494
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3247
          Classifications: {'peptide': 430}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 414}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.82, per 1000 atoms: 0.28
  Number of scatterers: 6494
  At special positions: 0
  Unit cell: (96.46, 94.34, 65.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1238      8.00
     N    1172      7.00
     C    4054      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: 0.51
  Conformation dependent library (CDL) restraints added in 386.7 milliseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      48.6% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 348 through 363
      removed outlier: 3.862A  pdb=" N   ALA A 352 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 384
      removed outlier: 3.883A  pdb=" N   GLN A 369 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ARG A 370 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA A 371 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 403
      removed outlier: 4.293A  pdb=" N   ILE A 388 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   LYS A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   SER A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 412
    Processing helix  chain 'A' and resid 415 through 433
    Processing helix  chain 'A' and resid 471 through 483
      removed outlier: 4.157A  pdb=" N   GLN A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 512
      removed outlier: 3.647A  pdb=" N   THR A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 534
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 579 through 592
    Processing helix  chain 'A' and resid 609 through 613
    Processing helix  chain 'A' and resid 614 through 626
    Processing helix  chain 'A' and resid 633 through 640
      removed outlier: 3.505A  pdb=" N   LEU A 640 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 678
    Processing helix  chain 'A' and resid 689 through 700
    Processing helix  chain 'A' and resid 740 through 744
      removed outlier: 3.671A  pdb=" N   LEU A 744 " --> pdb=" O   GLU A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 761
      removed outlier: 3.580A  pdb=" N   PHE A 760 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 363
      removed outlier: 3.862A  pdb=" N   ALA B 352 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 384
      removed outlier: 3.883A  pdb=" N   GLN B 369 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ARG B 370 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA B 371 " --> pdb=" O   PRO B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 403
      removed outlier: 4.293A  pdb=" N   ILE B 388 " --> pdb=" O   ARG B 384 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   LYS B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   SER B 402 " --> pdb=" O   GLU B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 412
    Processing helix  chain 'B' and resid 415 through 433
    Processing helix  chain 'B' and resid 471 through 483
      removed outlier: 4.157A  pdb=" N   GLN B 475 " --> pdb=" O   ASP B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 512
      removed outlier: 3.647A  pdb=" N   THR B 512 " --> pdb=" O   GLU B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 534
    Processing helix  chain 'B' and resid 546 through 557
    Processing helix  chain 'B' and resid 579 through 592
    Processing helix  chain 'B' and resid 609 through 613
    Processing helix  chain 'B' and resid 614 through 626
    Processing helix  chain 'B' and resid 633 through 640
      removed outlier: 3.505A  pdb=" N   LEU B 640 " --> pdb=" O   LEU B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 678
    Processing helix  chain 'B' and resid 689 through 700
    Processing helix  chain 'B' and resid 740 through 744
      removed outlier: 3.671A  pdb=" N   LEU B 744 " --> pdb=" O   GLU B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 757 through 761
      removed outlier: 3.580A  pdb=" N   PHE B 760 " --> pdb=" O   ALA B 757 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 771 through 772
      removed outlier: 3.515A  pdb=" N   GLU A 771 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG A 445 " --> pdb=" O   GLU A 771 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LEU A 450 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU A 451 " --> pdb=" O   GLU A 751 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A 751 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A 455 " --> pdb=" O   LYS A 747 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A 745 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 8.705A  pdb=" N   VAL B 705 " --> pdb=" O   THR A 746 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TRP A 748 " --> pdb=" O   VAL B 705 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488
      removed outlier: 6.306A  pdb=" N   LEU A 462 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   VAL A 461 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ILE A 542 " --> pdb=" O   VAL A 461 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU A 463 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 574
      removed outlier: 6.728A  pdb=" N   HIS A 571 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   VAL A 686 " --> pdb=" O   HIS A 571 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   TYR A 573 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 607
      removed outlier: 6.103A  pdb=" N   ILE A 606 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 630
      removed outlier: 6.871A  pdb=" N   LYS A 629 " --> pdb=" O   CYS A 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 705
      removed outlier: 3.527A  pdb=" N   THR B 745 " --> pdb=" O   VAL B 457 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B 455 " --> pdb=" O   LYS B 747 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU B 751 " --> pdb=" O   GLU B 451 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU B 451 " --> pdb=" O   GLU B 751 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LEU B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B 445 " --> pdb=" O   GLU B 771 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU B 771 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728
      removed outlier: 4.252A  pdb=" N   GLY A 726 " --> pdb=" O   VAL A 738 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 487 through 488
      removed outlier: 6.306A  pdb=" N   LEU B 462 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   VAL B 461 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ILE B 542 " --> pdb=" O   VAL B 461 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU B 463 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 571 through 574
      removed outlier: 6.728A  pdb=" N   HIS B 571 " --> pdb=" O   VAL B 684 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   VAL B 686 " --> pdb=" O   HIS B 571 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   TYR B 573 " --> pdb=" O   VAL B 686 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 605 through 607
      removed outlier: 6.103A  pdb=" N   ILE B 606 " --> pdb=" O   VAL B 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 629 through 630
      removed outlier: 6.871A  pdb=" N   LYS B 629 " --> pdb=" O   CYS B 659 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 726 through 728
      removed outlier: 4.252A  pdb=" N   GLY B 726 " --> pdb=" O   VAL B 738 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    822 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: 0.95

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2258
        1.34 -     1.46: 852
        1.46 -     1.57: 3438
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 6594
  Sorted by residual:
  bond pdb=" CA  PHE A 719 "
       pdb=" C   PHE A 719 "
    ideal  model  delta    sigma   weight residual
    1.522  1.493  0.028 1.72e-02 3.38e+03 2.70e+00
  bond pdb=" CA  PHE B 719 "
       pdb=" C   PHE B 719 "
    ideal  model  delta    sigma   weight residual
    1.522  1.493  0.028 1.72e-02 3.38e+03 2.70e+00
  bond pdb=" C   ARG B 469 "
       pdb=" N   PRO B 470 "
    ideal  model  delta    sigma   weight residual
    1.337  1.321  0.015 9.80e-03 1.04e+04 2.40e+00
  bond pdb=" C   ARG A 469 "
       pdb=" N   PRO A 470 "
    ideal  model  delta    sigma   weight residual
    1.337  1.321  0.015 9.80e-03 1.04e+04 2.40e+00
  bond pdb=" CB  VAL A 738 "
       pdb=" CG1 VAL A 738 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.14e+00
  ... (remaining 6589 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 8588
        1.75 -     3.50: 280
        3.50 -     5.25: 52
        5.25 -     7.00: 6
        7.00 -     8.75: 2
  Bond angle restraints: 8928
  Sorted by residual:
  angle pdb=" C   ALA B 518 "
        pdb=" N   VAL B 519 "
        pdb=" CA  VAL B 519 "
      ideal   model   delta    sigma   weight residual
     121.95  127.85   -5.90 1.53e+00 4.27e-01 1.49e+01
  angle pdb=" C   ALA A 518 "
        pdb=" N   VAL A 519 "
        pdb=" CA  VAL A 519 "
      ideal   model   delta    sigma   weight residual
     121.95  127.85   -5.90 1.53e+00 4.27e-01 1.49e+01
  angle pdb=" N   VAL B 519 "
        pdb=" CA  VAL B 519 "
        pdb=" C   VAL B 519 "
      ideal   model   delta    sigma   weight residual
     108.06  103.51    4.55 1.28e+00 6.10e-01 1.26e+01
  angle pdb=" N   VAL A 519 "
        pdb=" CA  VAL A 519 "
        pdb=" C   VAL A 519 "
      ideal   model   delta    sigma   weight residual
     108.06  103.51    4.55 1.28e+00 6.10e-01 1.26e+01
  angle pdb=" C   HIS B 571 "
        pdb=" N   VAL B 572 "
        pdb=" CA  VAL B 572 "
      ideal   model   delta    sigma   weight residual
     122.96  120.00    2.96 9.50e-01 1.11e+00 9.72e+00
  ... (remaining 8923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3602
       17.92 -    35.85: 342
       35.85 -    53.77: 74
       53.77 -    71.69: 10
       71.69 -    89.61: 8
  Dihedral angle restraints: 4036
    sinusoidal: 1572
      harmonic: 2464
  Sorted by residual:
  dihedral pdb=" CA  ARG A 469 "
           pdb=" C   ARG A 469 "
           pdb=" N   PRO A 470 "
           pdb=" CA  PRO A 470 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  ARG B 469 "
           pdb=" C   ARG B 469 "
           pdb=" N   PRO B 470 "
           pdb=" CA  PRO B 470 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  ASP B 754 "
           pdb=" C   ASP B 754 "
           pdb=" N   HIS B 755 "
           pdb=" CA  HIS B 755 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.82  -17.18     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 4033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 628
       0.036 -    0.071: 288
       0.071 -    0.107: 106
       0.107 -    0.143: 20
       0.143 -    0.178: 4
  Chirality restraints: 1046
  Sorted by residual:
  chirality pdb=" CA  VAL A 519 "
            pdb=" N   VAL A 519 "
            pdb=" C   VAL A 519 "
            pdb=" CB  VAL A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.96e-01
  chirality pdb=" CA  VAL B 519 "
            pdb=" N   VAL B 519 "
            pdb=" C   VAL B 519 "
            pdb=" CB  VAL B 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.96e-01
  chirality pdb=" CB  THR A 524 "
            pdb=" CA  THR A 524 "
            pdb=" OG1 THR A 524 "
            pdb=" CG2 THR A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.79e-01
  ... (remaining 1043 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 457 "    0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO B 458 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 458 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 458 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 457 "   -0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO A 458 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 458 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 458 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 643 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO B 644 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 644 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 644 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 204
        2.68 -     3.23: 6872
        3.23 -     3.79: 9631
        3.79 -     4.34: 12156
        4.34 -     4.90: 20843
  Nonbonded interactions: 49706
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 429 "
            pdb=" OG  SER B 433 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" O   ILE A 429 "
            pdb=" OG  SER A 433 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" OG  SER A 546 "
            pdb=" OD1 ASP A 548 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OG  SER B 546 "
            pdb=" OD1 ASP B 548 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" O   CYS A 570 "
            pdb=" ND1 HIS A 571 "
     model   vdw
     2.245 3.120
  ... (remaining 49701 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.230
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
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      :  0.007   0.048   6594  Z= 0.301
  Angle     :  0.789   8.746   8928  Z= 0.433
  Chirality :  0.046   0.178   1046
  Planarity :  0.004   0.042   1170
  Dihedral  : 15.049  89.614   2440
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.62 %
    Favored  : 87.15 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  8.41 %
    Favored  : 91.30 %
  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: -4.85 (0.24), residues: 856
  helix: -1.83 (0.24), residues: 362
  sheet: -4.72 (0.30), residues: 120
  loop : -4.11 (0.26), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 735 
 TYR   0.012   0.002   TYR B 631 
 PHE   0.015   0.002   PHE B 642 
 TRP   0.005   0.002   TRP A 748 
 HIS   0.004   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 6594)
  covalent geometry    : angle       0.78882 ( 8928)
  hydrogen bonds       : bond        0.14894 (  286)
  hydrogen bonds       : angle       6.65979 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.8392 (t0) cc_final: 0.8191 (t70)
REVERT: A  694 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7878 (ttm170)
REVERT: A  724 GLU cc_start: 0.8415 (pp20) cc_final: 0.7712 (pp20)
REVERT: B  445 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.6696 (ttm-80)
REVERT: B  575 ASP cc_start: 0.8386 (t0) cc_final: 0.8167 (t70)
REVERT: B  724 GLU cc_start: 0.8359 (pp20) cc_final: 0.7629 (pp20)
  outliers start: 2
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0854
  time to fit residues: 14.8919
Evaluate side-chains
  94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 363 GLN
A 375 ASN
A 556 GLN
A 599 ASN
A 607 HIS
A 652 HIS
A 708 ASN
B 354 ASN
B 363 GLN
B 375 ASN
B 392 ASN
B 556 GLN
B 607 HIS
B 652 HIS
B 708 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.153405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.115962 restraints weight = 8857.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.121384 restraints weight = 5023.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.125252 restraints weight = 3510.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.127943 restraints weight = 2760.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.129865 restraints weight = 2325.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6594  Z= 0.133
  Angle     :  0.656   6.877   8928  Z= 0.337
  Chirality :  0.043   0.148   1046
  Planarity :  0.004   0.033   1170
  Dihedral  :  4.787  17.002    918
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.35 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.44 (0.27), residues: 856
  helix: -0.41 (0.27), residues: 372
  sheet: -3.90 (0.35), residues: 128
  loop : -3.74 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 445 
 TYR   0.006   0.001   TYR B 654 
 PHE   0.019   0.002   PHE B 387 
 TRP   0.008   0.001   TRP A 748 
 HIS   0.006   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6594)
  covalent geometry    : angle       0.65551 ( 8928)
  hydrogen bonds       : bond        0.03467 (  286)
  hydrogen bonds       : angle       4.66874 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8307 (m-40) cc_final: 0.7950 (m110)
REVERT: A  584 LEU cc_start: 0.9201 (tt) cc_final: 0.8723 (mt)
REVERT: A  625 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7643 (ttm110)
REVERT: A  654 TYR cc_start: 0.7952 (m-10) cc_final: 0.7723 (m-10)
REVERT: A  694 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7793 (ttp-110)
REVERT: A  712 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8269 (tpt90)
REVERT: A  724 GLU cc_start: 0.8438 (pp20) cc_final: 0.7922 (pp20)
REVERT: B  450 LEU cc_start: 0.7886 (tt) cc_final: 0.7477 (tp)
REVERT: B  508 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: B  584 LEU cc_start: 0.9185 (tt) cc_final: 0.8679 (mt)
REVERT: B  654 TYR cc_start: 0.7973 (m-10) cc_final: 0.7728 (m-10)
  outliers start: 17
  outliers final: 13
  residues processed: 136
  average time/residue: 0.0768
  time to fit residues: 14.0704
Evaluate side-chains
  114 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  615 ILE
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 7 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0870
   chunk 57 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
A 675 HIS
B 354 ASN
B 599 ASN
B 675 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.153594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.116554 restraints weight = 8771.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.121675 restraints weight = 5016.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.125553 restraints weight = 3542.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128292 restraints weight = 2777.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.130098 restraints weight = 2330.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6594  Z= 0.129
  Angle     :  0.621   6.898   8928  Z= 0.314
  Chirality :  0.043   0.206   1046
  Planarity :  0.003   0.025   1170
  Dihedral  :  4.550  15.343    918
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.94 %
    Favored  : 81.74 %
  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: -2.63 (0.28), residues: 856
  helix:  0.28 (0.28), residues: 374
  sheet: -3.30 (0.39), residues: 122
  loop : -3.45 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 445 
 TYR   0.005   0.001   TYR B 677 
 PHE   0.036   0.002   PHE A 387 
 TRP   0.007   0.001   TRP B 768 
 HIS   0.004   0.001   HIS A 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6594)
  covalent geometry    : angle       0.62069 ( 8928)
  hydrogen bonds       : bond        0.03185 (  286)
  hydrogen bonds       : angle       4.39154 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8349 (tm-30)
REVERT: A  584 LEU cc_start: 0.9156 (tt) cc_final: 0.8713 (mt)
REVERT: A  594 TYR cc_start: 0.8459 (t80) cc_final: 0.7895 (t80)
REVERT: A  601 MET cc_start: 0.7913 (tmm) cc_final: 0.7548 (tmm)
REVERT: A  654 TYR cc_start: 0.7859 (m-10) cc_final: 0.7625 (m-10)
REVERT: A  712 ARG cc_start: 0.8534 (tpt90) cc_final: 0.8273 (tpt90)
REVERT: A  724 GLU cc_start: 0.8473 (pp20) cc_final: 0.7960 (pp20)
REVERT: B  375 ASN cc_start: 0.8351 (m-40) cc_final: 0.7990 (m110)
REVERT: B  508 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8425 (tm-30)
REVERT: B  584 LEU cc_start: 0.9140 (tt) cc_final: 0.8692 (mt)
REVERT: B  601 MET cc_start: 0.7957 (tmm) cc_final: 0.7593 (tmm)
REVERT: B  654 TYR cc_start: 0.7868 (m-10) cc_final: 0.7556 (m-10)
REVERT: B  662 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7243 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 133
  average time/residue: 0.0711
  time to fit residues: 12.8900
Evaluate side-chains
  113 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0470
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0370
   chunk 14 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.5356

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 565 HIS
B 565 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.155258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.117821 restraints weight = 8781.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123186 restraints weight = 4951.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.127122 restraints weight = 3468.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.129831 restraints weight = 2701.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.131895 restraints weight = 2266.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6594  Z= 0.116
  Angle     :  0.604   6.947   8928  Z= 0.305
  Chirality :  0.042   0.175   1046
  Planarity :  0.003   0.026   1170
  Dihedral  :  4.298  14.222    918
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.55 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.29), residues: 856
  helix:  0.64 (0.28), residues: 374
  sheet: -3.08 (0.38), residues: 140
  loop : -3.25 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 551 
 TYR   0.003   0.001   TYR B 677 
 PHE   0.029   0.002   PHE A 387 
 TRP   0.006   0.001   TRP B 768 
 HIS   0.003   0.001   HIS B 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6594)
  covalent geometry    : angle       0.60354 ( 8928)
  hydrogen bonds       : bond        0.02879 (  286)
  hydrogen bonds       : angle       4.15918 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8325 (m-40) cc_final: 0.7965 (m110)
REVERT: A  534 MET cc_start: 0.7828 (mtm) cc_final: 0.7572 (mtp)
REVERT: A  573 TYR cc_start: 0.8828 (t80) cc_final: 0.8362 (t80)
REVERT: A  584 LEU cc_start: 0.9119 (tt) cc_final: 0.8731 (mt)
REVERT: A  601 MET cc_start: 0.7886 (tmm) cc_final: 0.7515 (tmm)
REVERT: A  654 TYR cc_start: 0.7754 (m-10) cc_final: 0.7457 (m-10)
REVERT: A  724 GLU cc_start: 0.8471 (pp20) cc_final: 0.7936 (pp20)
REVERT: B  375 ASN cc_start: 0.8387 (m-40) cc_final: 0.8017 (m110)
REVERT: B  534 MET cc_start: 0.7793 (mtm) cc_final: 0.7572 (mtp)
REVERT: B  573 TYR cc_start: 0.8869 (t80) cc_final: 0.8388 (t80)
REVERT: B  584 LEU cc_start: 0.9126 (tt) cc_final: 0.8685 (mt)
REVERT: B  601 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7579 (tmm)
REVERT: B  654 TYR cc_start: 0.7774 (m-10) cc_final: 0.7423 (m-10)
REVERT: B  662 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7238 (tm-30)
REVERT: B  694 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7853 (ttp-110)
  outliers start: 18
  outliers final: 13
  residues processed: 134
  average time/residue: 0.0775
  time to fit residues: 14.1383
Evaluate side-chains
  128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  601 MET
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0670
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.6718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.154795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.117199 restraints weight = 8825.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.122676 restraints weight = 4934.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.126597 restraints weight = 3425.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.129258 restraints weight = 2669.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.131319 restraints weight = 2245.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6594  Z= 0.128
  Angle     :  0.608   8.960   8928  Z= 0.307
  Chirality :  0.042   0.163   1046
  Planarity :  0.003   0.026   1170
  Dihedral  :  4.266  13.453    918
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.70 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.08 (0.29), residues: 856
  helix:  0.66 (0.28), residues: 380
  sheet: -2.84 (0.39), residues: 140
  loop : -3.17 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 625 
 TYR   0.004   0.001   TYR B 654 
 PHE   0.023   0.002   PHE A 387 
 TRP   0.007   0.001   TRP B 768 
 HIS   0.003   0.001   HIS B 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6594)
  covalent geometry    : angle       0.60781 ( 8928)
  hydrogen bonds       : bond        0.02981 (  286)
  hydrogen bonds       : angle       4.12362 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  375 ASN cc_start: 0.8303 (m-40) cc_final: 0.7970 (m110)
REVERT: A  573 TYR cc_start: 0.8828 (t80) cc_final: 0.8426 (t80)
REVERT: A  584 LEU cc_start: 0.9138 (tt) cc_final: 0.8758 (mt)
REVERT: A  594 TYR cc_start: 0.8330 (t80) cc_final: 0.7764 (t80)
REVERT: A  601 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7405 (tmm)
REVERT: A  654 TYR cc_start: 0.7794 (m-10) cc_final: 0.7446 (m-10)
REVERT: A  712 ARG cc_start: 0.8620 (tpt90) cc_final: 0.8330 (tpt90)
REVERT: A  724 GLU cc_start: 0.8571 (pp20) cc_final: 0.8106 (pp20)
REVERT: B  573 TYR cc_start: 0.8863 (t80) cc_final: 0.8434 (t80)
REVERT: B  584 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8716 (mt)
REVERT: B  601 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7590 (tmm)
REVERT: B  624 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8724 (pttp)
REVERT: B  662 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7229 (tm-30)
REVERT: B  694 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7815 (ttp-110)
  outliers start: 21
  outliers final: 13
  residues processed: 123
  average time/residue: 0.0713
  time to fit residues: 12.2294
Evaluate side-chains
  120 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  601 MET
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    0.0670
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 85 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.155326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117662 restraints weight = 8758.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123203 restraints weight = 4887.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.127177 restraints weight = 3387.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.129996 restraints weight = 2633.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.131769 restraints weight = 2201.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6594  Z= 0.122
  Angle     :  0.604   9.520   8928  Z= 0.303
  Chirality :  0.042   0.180   1046
  Planarity :  0.003   0.025   1170
  Dihedral  :  4.198  13.270    918
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.99 %
    Favored  : 77.83 %
  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: -1.85 (0.29), residues: 856
  helix:  0.78 (0.28), residues: 380
  sheet: -2.39 (0.42), residues: 132
  loop : -3.15 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 625 
 TYR   0.004   0.001   TYR B 654 
 PHE   0.022   0.002   PHE B 387 
 TRP   0.006   0.001   TRP B 768 
 HIS   0.003   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6594)
  covalent geometry    : angle       0.60429 ( 8928)
  hydrogen bonds       : bond        0.02837 (  286)
  hydrogen bonds       : angle       4.06121 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  375 ASN cc_start: 0.8303 (m-40) cc_final: 0.7959 (m110)
REVERT: A  503 MET cc_start: 0.8247 (tpp) cc_final: 0.8037 (mmm)
REVERT: A  573 TYR cc_start: 0.8816 (t80) cc_final: 0.8505 (t80)
REVERT: A  584 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8760 (mt)
REVERT: A  594 TYR cc_start: 0.8296 (t80) cc_final: 0.7766 (t80)
REVERT: A  601 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7406 (tmm)
REVERT: A  654 TYR cc_start: 0.7778 (m-10) cc_final: 0.7417 (m-10)
REVERT: A  712 ARG cc_start: 0.8631 (tpt90) cc_final: 0.8337 (tpt90)
REVERT: A  724 GLU cc_start: 0.8586 (pp20) cc_final: 0.8119 (pp20)
REVERT: B  573 TYR cc_start: 0.8849 (t80) cc_final: 0.8457 (t80)
REVERT: B  584 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8717 (mt)
REVERT: B  601 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7583 (tmm)
REVERT: B  624 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8719 (pttp)
REVERT: B  662 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7240 (tm-30)
REVERT: B  694 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7789 (ttp-110)
  outliers start: 22
  outliers final: 11
  residues processed: 125
  average time/residue: 0.0730
  time to fit residues: 12.6750
Evaluate side-chains
  116 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  601 MET
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0070
   chunk 78 optimal weight:    0.4980
   chunk 23 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.155873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118439 restraints weight = 8616.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.123944 restraints weight = 4828.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.127905 restraints weight = 3350.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.130691 restraints weight = 2611.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.132721 restraints weight = 2183.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6594  Z= 0.119
  Angle     :  0.609   9.749   8928  Z= 0.303
  Chirality :  0.042   0.181   1046
  Planarity :  0.003   0.025   1170
  Dihedral  :  4.153  12.859    918
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 18.70 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.29), residues: 856
  helix:  0.81 (0.28), residues: 380
  sheet: -2.24 (0.42), residues: 132
  loop : -3.05 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 625 
 TYR   0.005   0.001   TYR B 654 
 PHE   0.028   0.002   PHE B 387 
 TRP   0.005   0.001   TRP A 748 
 HIS   0.004   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6594)
  covalent geometry    : angle       0.60938 ( 8928)
  hydrogen bonds       : bond        0.02842 (  286)
  hydrogen bonds       : angle       4.05235 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  375 ASN cc_start: 0.8293 (m-40) cc_final: 0.7942 (m110)
REVERT: A  573 TYR cc_start: 0.8802 (t80) cc_final: 0.8557 (t80)
REVERT: A  584 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8755 (mt)
REVERT: A  594 TYR cc_start: 0.8281 (t80) cc_final: 0.7787 (t80)
REVERT: A  601 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7421 (tmm)
REVERT: A  654 TYR cc_start: 0.7830 (m-10) cc_final: 0.7360 (m-10)
REVERT: A  712 ARG cc_start: 0.8615 (tpt90) cc_final: 0.8331 (tpt90)
REVERT: A  724 GLU cc_start: 0.8585 (pp20) cc_final: 0.8117 (pp20)
REVERT: B  503 MET cc_start: 0.8319 (mmm) cc_final: 0.8032 (mmm)
REVERT: B  508 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8535 (tm-30)
REVERT: B  573 TYR cc_start: 0.8835 (t80) cc_final: 0.8448 (t80)
REVERT: B  584 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8751 (mt)
REVERT: B  601 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7562 (tmm)
REVERT: B  624 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8684 (pttp)
REVERT: B  662 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7219 (tm-30)
REVERT: B  694 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7780 (ttp-110)
  outliers start: 25
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0704
  time to fit residues: 11.7404
Evaluate side-chains
  118 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  601 MET
Chi-restraints excluded: chain B residue  615 ILE
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0270
   chunk 66 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6838

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.155456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.118221 restraints weight = 8667.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.123507 restraints weight = 4843.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.127475 restraints weight = 3363.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.130264 restraints weight = 2614.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.132100 restraints weight = 2189.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6594  Z= 0.127
  Angle     :  0.637   8.865   8928  Z= 0.311
  Chirality :  0.043   0.178   1046
  Planarity :  0.003   0.025   1170
  Dihedral  :  4.143  12.973    918
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 18.99 %
    Favored  : 77.39 %
  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: -1.68 (0.29), residues: 856
  helix:  0.82 (0.28), residues: 380
  sheet: -2.17 (0.42), residues: 132
  loop : -2.98 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 625 
 TYR   0.006   0.001   TYR B 654 
 PHE   0.029   0.003   PHE A 616 
 TRP   0.005   0.001   TRP A 748 
 HIS   0.005   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6594)
  covalent geometry    : angle       0.63669 ( 8928)
  hydrogen bonds       : bond        0.02824 (  286)
  hydrogen bonds       : angle       4.02190 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8285 (m-40) cc_final: 0.7906 (m110)
REVERT: A  503 MET cc_start: 0.8256 (tpp) cc_final: 0.8005 (mmm)
REVERT: A  508 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8398 (tm-30)
REVERT: A  584 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8764 (mt)
REVERT: A  594 TYR cc_start: 0.8267 (t80) cc_final: 0.7749 (t80)
REVERT: A  601 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7534 (tmm)
REVERT: A  712 ARG cc_start: 0.8620 (tpt90) cc_final: 0.8347 (tpt90)
REVERT: A  724 GLU cc_start: 0.8586 (pp20) cc_final: 0.8107 (pp20)
REVERT: B  508 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8539 (tm-30)
REVERT: B  563 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8045 (tt)
REVERT: B  573 TYR cc_start: 0.8814 (t80) cc_final: 0.8454 (t80)
REVERT: B  584 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8723 (mt)
REVERT: B  601 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7591 (tmm)
REVERT: B  624 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8697 (pttp)
REVERT: B  662 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: B  694 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7786 (ttp-110)
  outliers start: 25
  outliers final: 15
  residues processed: 119
  average time/residue: 0.0637
  time to fit residues: 10.7205
Evaluate side-chains
  119 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  601 MET
Chi-restraints excluded: chain B residue  615 ILE
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 23 optimal weight:    0.4980
   chunk 69 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.155595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.118369 restraints weight = 8795.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.123934 restraints weight = 4882.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.127933 restraints weight = 3362.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.130717 restraints weight = 2611.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.132759 restraints weight = 2182.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6594  Z= 0.127
  Angle     :  0.634   8.410   8928  Z= 0.313
  Chirality :  0.043   0.170   1046
  Planarity :  0.003   0.025   1170
  Dihedral  :  4.141  12.933    918
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.71 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.61 (0.29), residues: 856
  helix:  0.83 (0.28), residues: 380
  sheet: -2.09 (0.43), residues: 132
  loop : -2.90 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 625 
 TYR   0.022   0.002   TYR A 573 
 PHE   0.025   0.002   PHE B 387 
 TRP   0.005   0.001   TRP A 748 
 HIS   0.005   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6594)
  covalent geometry    : angle       0.63436 ( 8928)
  hydrogen bonds       : bond        0.02816 (  286)
  hydrogen bonds       : angle       4.00317 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8279 (m-40) cc_final: 0.7908 (m110)
REVERT: A  503 MET cc_start: 0.8251 (tpp) cc_final: 0.8014 (mmm)
REVERT: A  508 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8384 (tm-30)
REVERT: A  584 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8762 (mt)
REVERT: A  594 TYR cc_start: 0.8241 (t80) cc_final: 0.7766 (t80)
REVERT: A  601 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7417 (tmm)
REVERT: A  654 TYR cc_start: 0.7813 (m-10) cc_final: 0.7520 (m-10)
REVERT: A  694 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7991 (ttp-110)
REVERT: A  712 ARG cc_start: 0.8604 (tpt90) cc_final: 0.8330 (tpt90)
REVERT: A  724 GLU cc_start: 0.8580 (pp20) cc_final: 0.8108 (pp20)
REVERT: B  503 MET cc_start: 0.7935 (mmm) cc_final: 0.7488 (tpp)
REVERT: B  508 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8512 (tm-30)
REVERT: B  521 LEU cc_start: 0.8157 (tt) cc_final: 0.7856 (tt)
REVERT: B  563 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8070 (tt)
REVERT: B  573 TYR cc_start: 0.8816 (t80) cc_final: 0.8439 (t80)
REVERT: B  584 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8725 (mt)
REVERT: B  601 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7591 (tmm)
REVERT: B  624 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8690 (pttp)
REVERT: B  662 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7296 (tm-30)
REVERT: B  694 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7780 (ttp-110)
  outliers start: 23
  outliers final: 15
  residues processed: 119
  average time/residue: 0.0648
  time to fit residues: 10.9146
Evaluate side-chains
  120 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  751 GLU
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  601 MET
Chi-restraints excluded: chain B residue  615 ILE
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  704 CYS
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0770
   chunk 37 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0370
   overall best weight:    0.4616

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.157271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.120403 restraints weight = 8599.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.126027 restraints weight = 4754.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.130032 restraints weight = 3263.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.132806 restraints weight = 2529.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.134899 restraints weight = 2102.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6594  Z= 0.115
  Angle     :  0.642   8.281   8928  Z= 0.315
  Chirality :  0.043   0.231   1046
  Planarity :  0.003   0.026   1170
  Dihedral  :  4.029  12.929    918
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.59 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.29), residues: 856
  helix:  0.90 (0.28), residues: 380
  sheet: -1.96 (0.43), residues: 134
  loop : -2.80 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 625 
 TYR   0.019   0.001   TYR A 573 
 PHE   0.024   0.002   PHE B 387 
 TRP   0.010   0.001   TRP B 768 
 HIS   0.005   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6594)
  covalent geometry    : angle       0.64205 ( 8928)
  hydrogen bonds       : bond        0.02654 (  286)
  hydrogen bonds       : angle       3.97046 (  822)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8308 (m-40) cc_final: 0.7976 (m110)
REVERT: A  503 MET cc_start: 0.8247 (tpp) cc_final: 0.7946 (mmm)
REVERT: A  584 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8747 (mt)
REVERT: A  594 TYR cc_start: 0.8213 (t80) cc_final: 0.7740 (t80)
REVERT: A  601 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7520 (tmm)
REVERT: A  654 TYR cc_start: 0.7653 (m-10) cc_final: 0.7323 (m-10)
REVERT: A  694 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.7994 (ttp-110)
REVERT: A  712 ARG cc_start: 0.8555 (tpt90) cc_final: 0.8278 (tpt90)
REVERT: A  724 GLU cc_start: 0.8600 (pp20) cc_final: 0.8127 (pp20)
REVERT: B  503 MET cc_start: 0.8016 (mmm) cc_final: 0.7729 (tpp)
REVERT: B  521 LEU cc_start: 0.8148 (tt) cc_final: 0.7861 (tt)
REVERT: B  563 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8044 (tt)
REVERT: B  573 TYR cc_start: 0.8804 (t80) cc_final: 0.8441 (t80)
REVERT: B  584 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8599 (mt)
REVERT: B  601 MET cc_start: 0.7940 (tmm) cc_final: 0.7553 (tmm)
REVERT: B  624 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8705 (pttp)
REVERT: B  662 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7222 (tm-30)
REVERT: B  694 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7781 (ttp-110)
  outliers start: 17
  outliers final: 11
  residues processed: 122
  average time/residue: 0.0669
  time to fit residues: 11.6280
Evaluate side-chains
  120 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  601 MET
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  476 VAL
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  684 VAL
Chi-restraints excluded: chain B residue  704 CYS
Chi-restraints excluded: chain B residue  745 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 33 optimal weight:    0.0670
   chunk 64 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.7724

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

Flipped N/Q/H residues before XYZ refinement:
** A 755 HIS ** 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 = 0.3873 r_free = 0.3873 target = 0.154504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.117650 restraints weight = 8606.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.123144 restraints weight = 4711.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.127073 restraints weight = 3242.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.129801 restraints weight = 2513.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.131738 restraints weight = 2097.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6594  Z= 0.141
  Angle     :  0.667   7.905   8928  Z= 0.329
  Chirality :  0.043   0.220   1046
  Planarity :  0.003   0.027   1170
  Dihedral  :  4.118  13.116    918
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 22.32 %
    Favored  : 75.22 %
  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: -1.57 (0.29), residues: 856
  helix:  0.75 (0.28), residues: 380
  sheet: -1.90 (0.44), residues: 132
  loop : -2.80 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 445 
 TYR   0.015   0.001   TYR A 573 
 PHE   0.043   0.003   PHE A 616 
 TRP   0.017   0.002   TRP A 768 
 HIS   0.002   0.001   HIS B 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6594)
  covalent geometry    : angle       0.66693 ( 8928)
  hydrogen bonds       : bond        0.02999 (  286)
  hydrogen bonds       : angle       4.04894 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1186.02 seconds
wall clock time: 21 minutes 11.29 seconds (1271.29 seconds total)