Starting phenix.real_space_refine
on Thu Jun  5 17:54:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wxf_32877/06_2025/7wxf_32877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxf_32877/06_2025/7wxf_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxf_32877/06_2025/7wxf_32877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxf_32877/06_2025/7wxf_32877.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxf_32877/06_2025/7wxf_32877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxf_32877/06_2025/7wxf_32877.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.88, per 1000 atoms: 0.91
  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: 1.57
  Conformation dependent library (CDL) restraints added in 945.4 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: 0.78
  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: 2.06

  Time building geometry restraints manager: 1.86 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: 0.03
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:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.570
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.470
-------------------------------------------------------------------------------
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 : 13.40
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.005   0.002   TRP A 748 
 HIS   0.004   0.001   HIS B 607 
 PHE   0.015   0.002   PHE B 642 
 TYR   0.012   0.002   TYR B 631 
 ARG   0.006   0.001   ARG A 735 

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

*********************** 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  : 0.793 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.8392 (t0) cc_final: 0.8191 (t70)
REVERT: A  694 ARG cc_start: 0.8127 (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: 0.8385 (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: 0.1910
  time to fit residues: 33.2535
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  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 559 HIS
A 607 HIS
A 652 HIS
** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 708 ASN
B 354 ASN
B 363 GLN
B 375 ASN
B 392 ASN
B 556 GLN
B 559 HIS
B 607 HIS
B 652 HIS
** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 708 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.149674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.112800 restraints weight = 8850.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.117923 restraints weight = 5084.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.121602 restraints weight = 3593.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6594  Z= 0.193
  Angle     :  0.704   7.285   8928  Z= 0.363
  Chirality :  0.044   0.148   1046
  Planarity :  0.004   0.034   1170
  Dihedral  :  5.063  18.160    918
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.07 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.27), residues: 856
  helix: -0.59 (0.27), residues: 372
  sheet: -3.81 (0.37), residues: 118
  loop : -3.78 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 748 
 HIS   0.006   0.001   HIS B 559 
 PHE   0.019   0.003   PHE B 387 
 TYR   0.006   0.002   TYR B 654 
 ARG   0.005   0.000   ARG A 445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  286)
  hydrogen bonds       : angle       4.84177 (  822)
  covalent geometry    : bond        0.00458 ( 6594)
  covalent geometry    : angle       0.70412 ( 8928)

*********************** 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
  123 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  625 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7608 (ttm110)
REVERT: A  724 GLU cc_start: 0.8572 (pp20) cc_final: 0.7845 (pp20)
REVERT: B  450 LEU cc_start: 0.7981 (tt) cc_final: 0.7543 (tp)
  outliers start: 20
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1731
  time to fit residues: 28.8655
Evaluate side-chains
  104 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  528 ILE
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  528 ILE
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 68 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
A 599 ASN
** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.152768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.115201 restraints weight = 8831.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.120429 restraints weight = 5040.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.124175 restraints weight = 3546.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.2105

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= 0.140
  Angle     :  0.638   6.924   8928  Z= 0.325
  Chirality :  0.043   0.204   1046
  Planarity :  0.003   0.029   1170
  Dihedral  :  4.690  16.066    918
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.68 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.28), residues: 856
  helix:  0.06 (0.27), residues: 374
  sheet: -3.40 (0.39), residues: 122
  loop : -3.55 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 768 
 HIS   0.005   0.001   HIS A 571 
 PHE   0.032   0.003   PHE A 387 
 TYR   0.003   0.001   TYR B 594 
 ARG   0.004   0.000   ARG A 445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  286)
  hydrogen bonds       : angle       4.49175 (  822)
  covalent geometry    : bond        0.00327 ( 6594)
  covalent geometry    : angle       0.63843 ( 8928)

*********************** 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
  136 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8390 (tm-30)
REVERT: A  584 LEU cc_start: 0.9195 (tt) cc_final: 0.8723 (mt)
REVERT: A  601 MET cc_start: 0.7976 (ppp) cc_final: 0.7768 (tmm)
REVERT: A  654 TYR cc_start: 0.7934 (m-10) cc_final: 0.7652 (m-10)
REVERT: A  724 GLU cc_start: 0.8566 (pp20) cc_final: 0.7969 (pp20)
REVERT: B  503 MET cc_start: 0.8352 (mmm) cc_final: 0.7993 (mmm)
REVERT: B  508 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8426 (tm-30)
REVERT: B  584 LEU cc_start: 0.9186 (tt) cc_final: 0.8700 (mt)
REVERT: B  654 TYR cc_start: 0.7953 (m-10) cc_final: 0.7589 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 130
  average time/residue: 0.2252
  time to fit residues: 41.3239
Evaluate side-chains
  113 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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 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  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 7 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 354 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 = 0.3847 r_free = 0.3847 target = 0.151649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.114170 restraints weight = 8927.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.119289 restraints weight = 5085.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.123060 restraints weight = 3594.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6594  Z= 0.160
  Angle     :  0.646   7.621   8928  Z= 0.329
  Chirality :  0.043   0.170   1046
  Planarity :  0.004   0.026   1170
  Dihedral  :  4.647  15.614    918
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.29), residues: 856
  helix:  0.40 (0.28), residues: 374
  sheet: -3.15 (0.40), residues: 118
  loop : -3.34 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 748 
 HIS   0.005   0.001   HIS A 571 
 PHE   0.032   0.003   PHE A 387 
 TYR   0.004   0.001   TYR B 594 
 ARG   0.009   0.000   ARG A 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 (  286)
  hydrogen bonds       : angle       4.40102 (  822)
  covalent geometry    : bond        0.00377 ( 6594)
  covalent geometry    : angle       0.64608 ( 8928)

*********************** 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
  129 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8298 (m-40) cc_final: 0.7928 (m110)
REVERT: A  508 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8387 (tm-30)
REVERT: A  534 MET cc_start: 0.8013 (mtp) cc_final: 0.7681 (mtp)
REVERT: A  573 TYR cc_start: 0.8808 (t80) cc_final: 0.8432 (t80)
REVERT: A  584 LEU cc_start: 0.9195 (tt) cc_final: 0.8745 (mt)
REVERT: A  594 TYR cc_start: 0.8423 (t80) cc_final: 0.7792 (t80)
REVERT: A  724 GLU cc_start: 0.8561 (pp20) cc_final: 0.7945 (pp20)
REVERT: B  349 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7704 (mm-30)
REVERT: B  508 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8441 (tm-30)
REVERT: B  534 MET cc_start: 0.7761 (mtp) cc_final: 0.7439 (mtp)
REVERT: B  573 TYR cc_start: 0.8861 (t80) cc_final: 0.8427 (t80)
REVERT: B  584 LEU cc_start: 0.9178 (tt) cc_final: 0.8689 (mt)
REVERT: B  601 MET cc_start: 0.7986 (tmm) cc_final: 0.7649 (tmm)
REVERT: B  625 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7265 (ttm110)
REVERT: B  694 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7906 (ttp-110)
  outliers start: 20
  outliers final: 14
  residues processed: 126
  average time/residue: 0.1780
  time to fit residues: 31.4596
Evaluate side-chains
  116 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
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  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  476 VAL
Chi-restraints excluded: chain B residue  487 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  704 CYS
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 3 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    1.2386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.150250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.113856 restraints weight = 8849.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.118883 restraints weight = 5001.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.122574 restraints weight = 3505.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6594  Z= 0.180
  Angle     :  0.660   8.362   8928  Z= 0.335
  Chirality :  0.043   0.164   1046
  Planarity :  0.004   0.027   1170
  Dihedral  :  4.694  15.174    918
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.28 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.29), residues: 856
  helix:  0.50 (0.28), residues: 374
  sheet: -3.23 (0.39), residues: 124
  loop : -3.22 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 748 
 HIS   0.005   0.001   HIS B 571 
 PHE   0.026   0.003   PHE A 387 
 TYR   0.005   0.001   TYR A 654 
 ARG   0.004   0.000   ARG A 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03366 (  286)
  hydrogen bonds       : angle       4.41812 (  822)
  covalent geometry    : bond        0.00425 ( 6594)
  covalent geometry    : angle       0.65984 ( 8928)

*********************** 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
  130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: A  375 ASN cc_start: 0.8309 (m-40) cc_final: 0.7940 (m110)
REVERT: A  508 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8351 (tm-30)
REVERT: A  573 TYR cc_start: 0.8787 (t80) cc_final: 0.8427 (t80)
REVERT: A  584 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8760 (mt)
REVERT: A  594 TYR cc_start: 0.8378 (t80) cc_final: 0.7789 (t80)
REVERT: A  601 MET cc_start: 0.7999 (tmm) cc_final: 0.7578 (tmm)
REVERT: B  349 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7692 (mm-30)
REVERT: B  508 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8414 (tm-30)
REVERT: B  534 MET cc_start: 0.7780 (mtp) cc_final: 0.7408 (mtp)
REVERT: B  573 TYR cc_start: 0.8855 (t80) cc_final: 0.8483 (t80)
REVERT: B  584 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8708 (mt)
REVERT: B  601 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7628 (tmm)
REVERT: B  694 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7841 (ttp-110)
  outliers start: 27
  outliers final: 19
  residues processed: 123
  average time/residue: 0.2040
  time to fit residues: 34.8658
Evaluate side-chains
  117 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
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  584 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  685 ILE
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  745 THR
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  531 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  685 ILE
Chi-restraints excluded: chain B residue  704 CYS
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 65 optimal weight:    0.0670
   chunk 7 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0370
   chunk 41 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 565 HIS
B 755 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.155131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.117164 restraints weight = 8678.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.122526 restraints weight = 4894.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.126441 restraints weight = 3426.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2746

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= 0.115
  Angle     :  0.605   7.562   8928  Z= 0.304
  Chirality :  0.042   0.165   1046
  Planarity :  0.003   0.026   1170
  Dihedral  :  4.360  13.530    918
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.43 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.29), residues: 856
  helix:  0.78 (0.28), residues: 374
  sheet: -3.04 (0.39), residues: 140
  loop : -3.11 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 768 
 HIS   0.003   0.001   HIS B 559 
 PHE   0.023   0.002   PHE A 387 
 TYR   0.003   0.001   TYR B 654 
 ARG   0.011   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02767 (  286)
  hydrogen bonds       : angle       4.11296 (  822)
  covalent geometry    : bond        0.00264 ( 6594)
  covalent geometry    : angle       0.60521 ( 8928)

*********************** 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
  144 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8219 (m-40) cc_final: 0.7854 (m110)
REVERT: A  508 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8455 (tm-30)
REVERT: A  573 TYR cc_start: 0.8774 (t80) cc_final: 0.8441 (t80)
REVERT: A  584 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8745 (mt)
REVERT: A  594 TYR cc_start: 0.8348 (t80) cc_final: 0.7736 (t80)
REVERT: A  601 MET cc_start: 0.8026 (tmm) cc_final: 0.7583 (tmm)
REVERT: A  654 TYR cc_start: 0.7820 (m-10) cc_final: 0.7423 (m-10)
REVERT: A  712 ARG cc_start: 0.8572 (tpt90) cc_final: 0.8280 (tpt90)
REVERT: A  724 GLU cc_start: 0.8566 (pp20) cc_final: 0.8087 (pp20)
REVERT: B  349 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7749 (mm-30)
REVERT: B  375 ASN cc_start: 0.8360 (m-40) cc_final: 0.8002 (m110)
REVERT: B  503 MET cc_start: 0.8086 (mmm) cc_final: 0.7716 (mmm)
REVERT: B  534 MET cc_start: 0.7733 (mtp) cc_final: 0.7332 (mtm)
REVERT: B  573 TYR cc_start: 0.8820 (t80) cc_final: 0.8432 (t80)
REVERT: B  584 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8718 (mt)
REVERT: B  601 MET cc_start: 0.7996 (tmm) cc_final: 0.7659 (tmm)
REVERT: B  624 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8694 (pttt)
REVERT: B  654 TYR cc_start: 0.7925 (m-10) cc_final: 0.7401 (m-10)
REVERT: B  694 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7836 (ttp-110)
  outliers start: 23
  outliers final: 15
  residues processed: 136
  average time/residue: 0.2551
  time to fit residues: 47.1984
Evaluate side-chains
  127 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 1.764 
-------------------------------------------------------------------------------
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  584 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  704 CYS
Chi-restraints excluded: chain A residue  745 THR
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  531 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  745 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 48 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3857 r_free = 0.3857 target = 0.153414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.116505 restraints weight = 8668.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.121828 restraints weight = 4861.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.125620 restraints weight = 3381.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6594  Z= 0.134
  Angle     :  0.635   9.358   8928  Z= 0.315
  Chirality :  0.043   0.186   1046
  Planarity :  0.003   0.029   1170
  Dihedral  :  4.346  15.223    918
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.28 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.29), residues: 856
  helix:  0.71 (0.28), residues: 378
  sheet: -2.93 (0.40), residues: 140
  loop : -3.06 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 768 
 HIS   0.004   0.001   HIS B 559 
 PHE   0.020   0.002   PHE A 387 
 TYR   0.004   0.001   TYR B 594 
 ARG   0.007   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  286)
  hydrogen bonds       : angle       4.15291 (  822)
  covalent geometry    : bond        0.00315 ( 6594)
  covalent geometry    : angle       0.63535 ( 8928)

*********************** 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
  141 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8236 (m-40) cc_final: 0.7866 (m110)
REVERT: A  573 TYR cc_start: 0.8750 (t80) cc_final: 0.8428 (t80)
REVERT: A  584 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8755 (mt)
REVERT: A  594 TYR cc_start: 0.8317 (t80) cc_final: 0.7724 (t80)
REVERT: A  601 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7597 (tmm)
REVERT: A  654 TYR cc_start: 0.7938 (m-10) cc_final: 0.7436 (m-10)
REVERT: A  712 ARG cc_start: 0.8604 (tpt90) cc_final: 0.8302 (tpt90)
REVERT: A  724 GLU cc_start: 0.8562 (pp20) cc_final: 0.8104 (pp20)
REVERT: B  349 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7773 (mm-30)
REVERT: B  503 MET cc_start: 0.8218 (mmm) cc_final: 0.7732 (mmm)
REVERT: B  534 MET cc_start: 0.7730 (mtp) cc_final: 0.7322 (mtm)
REVERT: B  573 TYR cc_start: 0.8811 (t80) cc_final: 0.8435 (t80)
REVERT: B  584 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8727 (mt)
REVERT: B  601 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7674 (tmm)
REVERT: B  624 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8716 (pttp)
REVERT: B  694 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7831 (ttp-110)
REVERT: B  775 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7478 (pp)
  outliers start: 29
  outliers final: 19
  residues processed: 129
  average time/residue: 0.1628
  time to fit residues: 29.6917
Evaluate side-chains
  128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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  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  685 ILE
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  745 THR
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  531 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
Chi-restraints excluded: chain B residue  775 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3853 r_free = 0.3853 target = 0.152544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.114929 restraints weight = 8754.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.120170 restraints weight = 4989.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.123873 restraints weight = 3516.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6594  Z= 0.173
  Angle     :  0.666   8.662   8928  Z= 0.334
  Chirality :  0.044   0.177   1046
  Planarity :  0.003   0.027   1170
  Dihedral  :  4.493  15.720    918
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 20.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.29), residues: 856
  helix:  0.61 (0.28), residues: 380
  sheet: -2.99 (0.40), residues: 140
  loop : -3.09 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 768 
 HIS   0.004   0.001   HIS B 559 
 PHE   0.017   0.002   PHE A 466 
 TYR   0.008   0.001   TYR B 654 
 ARG   0.005   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  286)
  hydrogen bonds       : angle       4.24803 (  822)
  covalent geometry    : bond        0.00411 ( 6594)
  covalent geometry    : angle       0.66594 ( 8928)

*********************** 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: 29
    poor density    : 100
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  375 ASN cc_start: 0.8305 (m-40) cc_final: 0.7949 (m110)
REVERT: A  573 TYR cc_start: 0.8750 (t80) cc_final: 0.8420 (t80)
REVERT: A  584 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8764 (mt)
REVERT: A  594 TYR cc_start: 0.8340 (t80) cc_final: 0.7798 (t80)
REVERT: A  601 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7585 (tmm)
REVERT: B  349 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7694 (mm-30)
REVERT: B  503 MET cc_start: 0.8284 (mmm) cc_final: 0.7747 (mmm)
REVERT: B  534 MET cc_start: 0.7795 (mtp) cc_final: 0.7402 (mtp)
REVERT: B  573 TYR cc_start: 0.8811 (t80) cc_final: 0.8473 (t80)
REVERT: B  584 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8694 (mt)
REVERT: B  601 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7641 (tmm)
REVERT: B  694 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7840 (ttp-110)
REVERT: B  775 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7491 (pp)
  outliers start: 29
  outliers final: 20
  residues processed: 119
  average time/residue: 0.1401
  time to fit residues: 23.9755
Evaluate side-chains
  123 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  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  685 ILE
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  745 THR
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  531 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  685 ILE
Chi-restraints excluded: chain B residue  704 CYS
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  775 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    0.2980
   chunk 65 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 559 HIS
** B 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.152785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.115745 restraints weight = 8797.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.121097 restraints weight = 4916.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.124846 restraints weight = 3398.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6594  Z= 0.146
  Angle     :  0.650   8.298   8928  Z= 0.321
  Chirality :  0.043   0.170   1046
  Planarity :  0.003   0.026   1170
  Dihedral  :  4.399  15.265    918
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 21.01 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.29), residues: 856
  helix:  0.65 (0.28), residues: 380
  sheet: -2.90 (0.40), residues: 140
  loop : -2.98 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 748 
 HIS   0.005   0.001   HIS B 559 
 PHE   0.025   0.002   PHE B 616 
 TYR   0.007   0.001   TYR B 654 
 ARG   0.005   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03008 (  286)
  hydrogen bonds       : angle       4.19515 (  822)
  covalent geometry    : bond        0.00345 ( 6594)
  covalent geometry    : angle       0.64957 ( 8928)

*********************** 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
  141 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  375 ASN cc_start: 0.8243 (m-40) cc_final: 0.7875 (m110)
REVERT: A  573 TYR cc_start: 0.8739 (t80) cc_final: 0.8401 (t80)
REVERT: A  584 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8759 (mt)
REVERT: A  594 TYR cc_start: 0.8312 (t80) cc_final: 0.7745 (t80)
REVERT: A  601 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7479 (tmm)
REVERT: A  654 TYR cc_start: 0.7973 (m-10) cc_final: 0.7415 (m-10)
REVERT: B  349 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7760 (mm-30)
REVERT: B  503 MET cc_start: 0.8371 (mmm) cc_final: 0.7782 (mmm)
REVERT: B  534 MET cc_start: 0.7790 (mtp) cc_final: 0.7411 (mtm)
REVERT: B  563 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8130 (tt)
REVERT: B  573 TYR cc_start: 0.8791 (t80) cc_final: 0.8405 (t80)
REVERT: B  584 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8735 (mt)
REVERT: B  601 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7646 (tmm)
REVERT: B  654 TYR cc_start: 0.7942 (m-10) cc_final: 0.7552 (m-10)
REVERT: B  694 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7841 (ttp-110)
REVERT: B  775 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7444 (pp)
  outliers start: 34
  outliers final: 21
  residues processed: 128
  average time/residue: 0.1445
  time to fit residues: 25.9855
Evaluate side-chains
  130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  531 LEU
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  685 ILE
Chi-restraints excluded: chain A residue  704 CYS
Chi-restraints excluded: chain A residue  745 THR
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  531 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  685 ILE
Chi-restraints excluded: chain B residue  704 CYS
Chi-restraints excluded: chain B residue  745 THR
Chi-restraints excluded: chain B residue  775 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    0.0470
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.3478

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

Flipped N/Q/H residues before XYZ refinement:
A 559 HIS
B 755 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.157302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.120020 restraints weight = 8614.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.125385 restraints weight = 4910.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.129271 restraints weight = 3431.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6594  Z= 0.111
  Angle     :  0.653   8.158   8928  Z= 0.317
  Chirality :  0.043   0.174   1046
  Planarity :  0.003   0.026   1170
  Dihedral  :  4.134  13.790    918
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.32 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.29), residues: 856
  helix:  0.75 (0.28), residues: 380
  sheet: -2.67 (0.40), residues: 140
  loop : -2.89 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 768 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.032   0.002   PHE A 616 
 TYR   0.006   0.001   TYR B 654 
 ARG   0.004   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02658 (  286)
  hydrogen bonds       : angle       4.06401 (  822)
  covalent geometry    : bond        0.00254 ( 6594)
  covalent geometry    : angle       0.65287 ( 8928)

********************** 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
  135 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8212 (m-40) cc_final: 0.7868 (m110)
REVERT: A  573 TYR cc_start: 0.8706 (t80) cc_final: 0.8375 (t80)
REVERT: A  584 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8767 (mt)
REVERT: A  594 TYR cc_start: 0.8276 (t80) cc_final: 0.7698 (t80)
REVERT: A  601 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7565 (tmm)
REVERT: A  654 TYR cc_start: 0.7636 (m-10) cc_final: 0.7162 (m-10)
REVERT: A  724 GLU cc_start: 0.8599 (pp20) cc_final: 0.8211 (pp20)
REVERT: B  503 MET cc_start: 0.8333 (mmm) cc_final: 0.7730 (mmm)
REVERT: B  563 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8067 (tt)
REVERT: B  573 TYR cc_start: 0.8749 (t80) cc_final: 0.8377 (t80)
REVERT: B  584 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8721 (mt)
REVERT: B  601 MET cc_start: 0.7913 (tmm) cc_final: 0.7606 (tmm)
REVERT: B  624 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8700 (pttp)
REVERT: B  694 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7822 (ttp-110)
REVERT: B  775 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7441 (pp)
  outliers start: 22
  outliers final: 16
  residues processed: 127
  average time/residue: 0.1624
  time to fit residues: 28.5953
Evaluate side-chains
  125 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  531 LEU
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  704 CYS
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  563 LEU
Chi-restraints excluded: chain B residue  584 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
Chi-restraints excluded: chain B residue  775 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0030
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0370
   chunk 72 optimal weight:    0.0030
   chunk 28 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0170
   overall best weight:    0.0716

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.158084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.121659 restraints weight = 8625.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.127281 restraints weight = 4778.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.131366 restraints weight = 3269.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6594  Z= 0.109
  Angle     :  0.652  10.406   8928  Z= 0.313
  Chirality :  0.042   0.170   1046
  Planarity :  0.003   0.027   1170
  Dihedral  :  3.936  14.904    918
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 24.64 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.29), residues: 856
  helix:  0.87 (0.28), residues: 382
  sheet: -2.36 (0.41), residues: 140
  loop : -2.72 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 768 
 HIS   0.003   0.001   HIS B 559 
 PHE   0.019   0.002   PHE A 387 
 TYR   0.006   0.001   TYR B 573 
 ARG   0.005   0.000   ARG B 625 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02446 (  286)
  hydrogen bonds       : angle       3.97905 (  822)
  covalent geometry    : bond        0.00238 ( 6594)
  covalent geometry    : angle       0.65246 ( 8928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2547.81 seconds
wall clock time: 47 minutes 15.32 seconds (2835.32 seconds total)