Starting phenix.real_space_refine
on Wed Aug  5 01:08:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rwb_54306/08_2026/9rwb_54306.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rwb_54306/08_2026/9rwb_54306.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rwb_54306/08_2026/9rwb_54306.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rwb_54306/08_2026/9rwb_54306.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rwb_54306/08_2026/9rwb_54306.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rwb_54306/08_2026/9rwb_54306.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      97      5.49       5
     S      35      5.16       5
     C    4512      2.51       5
     N    1324      2.21       5
     O    1763      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7731
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 417
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 414
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 24
    Chain: "C"
      Number of atoms: 1216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1216
          Classifications: {'peptide': 152}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 147}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 3618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3618
          Classifications: {'peptide': 453}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 442}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 24
    Chain: "E"
      Number of atoms: 2066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2066
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 43, 'rna3p_pyr': 52}
          Link IDs: {'rna2p': 3, 'rna3p': 94}
          Chain breaks: 2
  Time building chain proxies: 1.65, per 1000 atoms: 0.21
  Number of scatterers: 7731
  At special positions: 0
  Unit cell: (77.307, 93.192, 154.614, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P      97     15.00
     O    1763      8.00
     N    1324      7.00
     C    4512      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 323.9 milliseconds
  

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      71.3% alpha, 9.1% beta
      36 base pairs and 68 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'C' and resid 6 through 25
      removed outlier: 3.692A  pdb=" N   LYS C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'C' and resid 36 through 39
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 53 through 63
    Processing helix  chain 'C' and resid 95 through 112
      removed outlier: 3.604A  pdb=" N   GLU C  99 " --> pdb=" O   ASP C  95 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY C 112 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.831A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 137
    Processing helix  chain 'C' and resid 140 through 152
    Processing helix  chain 'D' and resid 4 through 25
      removed outlier: 4.054A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 36
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 43 through 51
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.917A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 137
    Processing helix  chain 'D' and resid 140 through 152
      removed outlier: 3.774A  pdb=" N   HIS D 151 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 529
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.767A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 617 through 630
      removed outlier: 4.673A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 671
    Processing helix  chain 'D' and resid 676 through 688
      removed outlier: 3.853A  pdb=" N   GLN D 680 " --> pdb=" O   PRO D 676 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 689 through 693
      removed outlier: 4.225A  pdb=" N   TRP D 692 " --> pdb=" O   GLN D 689 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 3.767A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 714 through 725
      removed outlier: 3.933A  pdb=" N   GLN D 724 " --> pdb=" O   ASN D 720 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE D 725 " --> pdb=" O   LEU D 721 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 726 through 743
      removed outlier: 3.658A  pdb=" N   ALA D 731 " --> pdb=" O   PRO D 727 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU D 732 " --> pdb=" O   GLU D 728 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.666A  pdb=" N   VAL D 750 " --> pdb=" O   LYS D 746 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
      removed outlier: 3.579A  pdb=" N   ARG D 785 " --> pdb=" O   ASN D 781 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 793 through 802
      removed outlier: 4.199A  pdb=" N   GLY D 802 " --> pdb=" O   GLU D 798 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 803 through 815
    Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'C' and resid 116 through 117
    Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA4, first strand: chain 'D' and resid 155 through 158
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 533
      removed outlier: 6.948A  pdb=" N   GLU D 563 " --> pdb=" O   THR D 574 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 533
      removed outlier: 6.573A  pdb=" N   ILE D 556 " --> pdb=" O   ILE D 612 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   VAL D 614 " --> pdb=" O   ILE D 556 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL D 558 " --> pdb=" O   VAL D 614 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   PHE D 637 " --> pdb=" O   VAL D 611 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)

    382 hydrogen bonds defined for protein.
    1110 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      89 hydrogen bonds
      162 hydrogen bond angles
      0 basepair planarities
      36 basepair parallelities
      68 stacking parallelities
  Total time for adding SS restraints: 1.40

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1363
        1.33 -     1.45: 2394
        1.45 -     1.57: 4043
        1.57 -     1.70: 192
        1.70 -     1.82: 58
  Bond restraints: 8050
  Sorted by residual:
  bond pdb=" C   VAL C  75 "
       pdb=" O   VAL C  75 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.028 1.01e-02 9.80e+03 7.91e+00
  bond pdb=" C   TYR C  74 "
       pdb=" N   VAL C  75 "
    ideal  model  delta    sigma   weight residual
    1.330  1.367 -0.037 1.35e-02 5.49e+03 7.54e+00
  bond pdb=" CB  VAL D 133 "
       pdb=" CG2 VAL D 133 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.57e+00
  bond pdb=" N   CYS A 695 "
       pdb=" CA  CYS A 695 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.90e-02 2.77e+03 3.93e+00
  bond pdb=" CB  GLN D 610 "
       pdb=" CG  GLN D 610 "
    ideal  model  delta    sigma   weight residual
    1.520  1.571 -0.051 3.00e-02 1.11e+03 2.92e+00
  ... (remaining 8045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 10096
        1.76 -     3.51: 1096
        3.51 -     5.27: 91
        5.27 -     7.03: 20
        7.03 -     8.79: 4
  Bond angle restraints: 11307
  Sorted by residual:
  angle pdb=" O4'   U E  41 "
        pdb=" C1'   U E  41 "
        pdb=" N1    U E  41 "
      ideal   model   delta    sigma   weight residual
     108.50  112.57   -4.07 7.00e-01 2.04e+00 3.38e+01
  angle pdb=" C3'   C E  38 "
        pdb=" O3'   C E  38 "
        pdb=" P     U E  39 "
      ideal   model   delta    sigma   weight residual
     119.70  125.95   -6.25 1.20e+00 6.94e-01 2.71e+01
  angle pdb=" C2'   A E   3 "
        pdb=" C1'   A E   3 "
        pdb=" N9    A E   3 "
      ideal   model   delta    sigma   weight residual
     112.00  117.51   -5.51 1.10e+00 8.26e-01 2.51e+01
  angle pdb=" O5'   C E  38 "
        pdb=" C5'   C E  38 "
        pdb=" C4'   C E  38 "
      ideal   model   delta    sigma   weight residual
     109.40  113.37   -3.97 8.00e-01 1.56e+00 2.46e+01
  angle pdb=" C3'   A E  94 "
        pdb=" O3'   A E  94 "
        pdb=" P     G E  95 "
      ideal   model   delta    sigma   weight residual
     119.70  125.61   -5.91 1.20e+00 6.94e-01 2.43e+01
  ... (remaining 11302 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.20: 4783
       34.20 -    68.39: 240
       68.39 -   102.59: 31
      102.59 -   136.78: 3
      136.78 -   170.98: 1
  Dihedral angle restraints: 5058
    sinusoidal: 2969
      harmonic: 2089
  Sorted by residual:
  dihedral pdb=" CA  GLY D 112 "
           pdb=" C   GLY D 112 "
           pdb=" N   ALA D 113 "
           pdb=" CA  ALA D 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.67  -28.33     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  MET D 790 "
           pdb=" C   MET D 790 "
           pdb=" N   ASP D 791 "
           pdb=" CA  ASP D 791 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.71   26.29     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ASN C  78 "
           pdb=" C   ASN C  78 "
           pdb=" N   ALA C  79 "
           pdb=" CA  ALA C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.29   24.71     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 5055 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1057
       0.082 -    0.164: 278
       0.164 -    0.246: 20
       0.246 -    0.328: 3
       0.328 -    0.410: 2
  Chirality restraints: 1360
  Sorted by residual:
  chirality pdb=" CB  VAL C  75 "
            pdb=" CA  VAL C  75 "
            pdb=" CG1 VAL C  75 "
            pdb=" CG2 VAL C  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.41 2.00e-01 2.50e+01 4.19e+00
  chirality pdb=" C3'   A E  94 "
            pdb=" C4'   A E  94 "
            pdb=" O3'   A E  94 "
            pdb=" C2'   A E  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.15   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" C1'   G E 122 "
            pdb=" O4'   G E 122 "
            pdb=" C2'   G E 122 "
            pdb=" N9    G E 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.18    0.29 2.00e-01 2.50e+01 2.13e+00
  ... (remaining 1357 not shown)

  Planarity restraints: 1093
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E  86 "    0.020 2.00e-02 2.50e+03   3.27e-02 3.20e+01
        pdb=" N9    G E  86 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8    G E  86 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G E  86 "   -0.056 2.00e-02 2.50e+03
        pdb=" C5    G E  86 "    0.016 2.00e-02 2.50e+03
        pdb=" C6    G E  86 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G E  86 "    0.053 2.00e-02 2.50e+03
        pdb=" N1    G E  86 "   -0.058 2.00e-02 2.50e+03
        pdb=" C2    G E  86 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2    G E  86 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G E  86 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G E  86 "    0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E  34 "   -0.026 2.00e-02 2.50e+03   2.98e-02 2.67e+01
        pdb=" N9    G E  34 "    0.017 2.00e-02 2.50e+03
        pdb=" C8    G E  34 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G E  34 "    0.046 2.00e-02 2.50e+03
        pdb=" C5    G E  34 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G E  34 "    0.005 2.00e-02 2.50e+03
        pdb=" O6    G E  34 "   -0.059 2.00e-02 2.50e+03
        pdb=" N1    G E  34 "    0.048 2.00e-02 2.50e+03
        pdb=" C2    G E  34 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G E  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G E  34 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G E  34 "   -0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E  17 "   -0.007 2.00e-02 2.50e+03   2.95e-02 2.61e+01
        pdb=" N9    G E  17 "    0.014 2.00e-02 2.50e+03
        pdb=" C8    G E  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G E  17 "   -0.051 2.00e-02 2.50e+03
        pdb=" C5    G E  17 "    0.007 2.00e-02 2.50e+03
        pdb=" C6    G E  17 "    0.007 2.00e-02 2.50e+03
        pdb=" O6    G E  17 "    0.041 2.00e-02 2.50e+03
        pdb=" N1    G E  17 "   -0.058 2.00e-02 2.50e+03
        pdb=" C2    G E  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G E  17 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G E  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G E  17 "    0.049 2.00e-02 2.50e+03
  ... (remaining 1090 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 3203
        2.94 -     3.43: 7903
        3.43 -     3.92: 13760
        3.92 -     4.41: 15000
        4.41 -     4.90: 22325
  Nonbonded interactions: 62191
  Sorted by model distance:
  nonbonded pdb=" C   GLU D 572 "
            pdb=" OE1 GLU D 572 "
     model   vdw
     2.455 3.270
  nonbonded pdb=" OE1 GLU D 572 "
            pdb=" O   ILE D 573 "
     model   vdw
     2.476 3.040
  nonbonded pdb=" OE2 GLU D 762 "
            pdb=" NH1 ARG D 782 "
     model   vdw
     2.536 3.120
  nonbonded pdb=" O   GLU B 697 "
            pdb=" OG1 THR B 700 "
     model   vdw
     2.539 3.040
  nonbonded pdb=" N   GLN D 610 "
            pdb=" OE1 GLN D 610 "
     model   vdw
     2.542 3.120
  ... (remaining 62186 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 695 through 735 or (resid 736 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 737 through 747))
  selection = (chain 'B' and (resid 695 through 739 or (resid 740 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 741 through 747))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.020
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
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      :  0.005   0.085   8050  Z= 0.328
  Angle     :  1.081   8.786  11307  Z= 0.808
  Chirality :  0.068   0.410   1360
  Planarity :  0.011   0.108   1093
  Dihedral  : 18.736 170.977   3702
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  2.44 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 12.56 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.29), residues: 697
  helix: -0.49 (0.21), residues: 460
  sheet: -1.32 (0.96), residues: 25
  loop : -0.54 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.003   ARG C  20 
 TYR   0.053   0.007   TYR D  64 
 PHE   0.023   0.003   PHE D 637 
 TRP   0.010   0.004   TRP D 522 
 HIS   0.016   0.004   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00514 /  0.33 ( 8050)
  covalent geometry    : angle       1.08133 /  0.81 (11307)
  hydrogen bonds       : bond        0.11791 /  7.97 (  464)
  hydrogen bonds       : angle       6.38360 /  4.81 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7914 (tp30) cc_final: 0.7468 (tp30)
REVERT: A  746 MET cc_start: 0.4753 (mtt) cc_final: 0.3996 (ttp)
REVERT: C  132 GLN cc_start: 0.7434 (mt0) cc_final: 0.7147 (mp10)
REVERT: D  149 MET cc_start: 0.7993 (mmt) cc_final: 0.7792 (mmm)
REVERT: D  650 GLU cc_start: 0.7844 (tt0) cc_final: 0.7419 (tm-30)
REVERT: D  660 TYR cc_start: 0.8419 (m-80) cc_final: 0.8141 (m-10)
REVERT: D  666 LEU cc_start: 0.7583 (tp) cc_final: 0.7366 (tt)
REVERT: D  733 PHE cc_start: 0.7931 (t80) cc_final: 0.7668 (t80)
REVERT: D  743 MET cc_start: 0.8999 (tpt) cc_final: 0.8688 (tpt)
REVERT: D  790 MET cc_start: 0.8209 (mmm) cc_final: 0.8006 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.0836
  time to fit residues: 14.5819
Evaluate side-chains
  105 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 706 ASN
C  98 GLN
C 106 ASN
D 649 GLN
D 664 ASN
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.184554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.136895 restraints weight = 11870.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 3.68
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8050  Z= 0.173
  Angle     :  0.658   8.549  11307  Z= 0.369
  Chirality :  0.044   0.355   1360
  Planarity :  0.005   0.056   1093
  Dihedral  : 19.231 175.529   2291
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.30 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 11.24 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.31), residues: 697
  helix:  0.90 (0.23), residues: 458
  sheet: -1.11 (1.02), residues: 25
  loop : -0.49 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG D 799 
 TYR   0.031   0.002   TYR D 685 
 PHE   0.016   0.002   PHE C 147 
 TRP   0.006   0.001   TRP D 522 
 HIS   0.008   0.002   HIS D 714 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.17 ( 8050)
  covalent geometry    : angle       0.65831 /  0.37 (11307)
  hydrogen bonds       : bond        0.06681 /  4.41 (  464)
  hydrogen bonds       : angle       4.87637 /  3.65 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7690 (tp30) cc_final: 0.7286 (tp30)
REVERT: A  714 GLU cc_start: 0.8030 (tp30) cc_final: 0.7807 (tp30)
REVERT: C   76 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7020 (pm20)
REVERT: C  132 GLN cc_start: 0.7541 (mt0) cc_final: 0.7204 (mp10)
REVERT: D  109 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7469 (tt)
REVERT: D  743 MET cc_start: 0.8813 (tpt) cc_final: 0.8599 (tpt)
REVERT: D  790 MET cc_start: 0.7595 (mmm) cc_final: 0.7371 (mmm)
  outliers start: 26
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0725
  time to fit residues: 12.3080
Evaluate side-chains
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue    8 MET
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  531 THR
Chi-restraints excluded: chain D residue  532 VAL
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  565 ILE
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  752 ILE
Chi-restraints excluded: chain D residue  799 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 63 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 728 GLN
D 649 GLN
D 664 ASN
D 714 HIS
D 724 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.184143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.125007 restraints weight = 11820.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.22
r_work: 0.3298 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8050  Z= 0.131
  Angle     :  0.553   6.975  11307  Z= 0.313
  Chirality :  0.038   0.305   1360
  Planarity :  0.004   0.052   1093
  Dihedral  : 19.156 179.072   2291
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.73 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 13.72 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.31), residues: 697
  helix:  1.37 (0.24), residues: 458
  sheet: -0.86 (1.06), residues: 22
  loop : -0.32 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 724 
 TYR   0.038   0.002   TYR D 685 
 PHE   0.027   0.002   PHE D 691 
 TRP   0.007   0.001   TRP D 522 
 HIS   0.006   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.13 ( 8050)
  covalent geometry    : angle       0.55264 /  0.31 (11307)
  hydrogen bonds       : bond        0.05904 /  3.88 (  464)
  hydrogen bonds       : angle       4.43625 /  3.34 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7880 (tp30) cc_final: 0.7383 (tp30)
REVERT: A  714 GLU cc_start: 0.8348 (tp30) cc_final: 0.8127 (tp30)
REVERT: C  106 ASN cc_start: 0.8278 (m-40) cc_final: 0.8075 (m110)
REVERT: C  132 GLN cc_start: 0.7537 (mt0) cc_final: 0.7116 (mp10)
REVERT: C  163 MET cc_start: 0.2453 (mmm) cc_final: 0.2017 (mmm)
REVERT: D    4 MET cc_start: 0.6898 (tpt) cc_final: 0.6134 (tpp)
REVERT: D  109 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7798 (tt)
REVERT: D  586 PHE cc_start: 0.5694 (m-80) cc_final: 0.5333 (m-80)
REVERT: D  780 SER cc_start: 0.8304 (m) cc_final: 0.8007 (p)
  outliers start: 22
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0800
  time to fit residues: 13.2737
Evaluate side-chains
  110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  531 THR
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  649 GLN
Chi-restraints excluded: chain D residue  666 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 70 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 728 GLN
** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 664 ASN
D 748 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.183507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.122017 restraints weight = 11974.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.30
r_work: 0.3276 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8050  Z= 0.133
  Angle     :  0.537   6.697  11307  Z= 0.300
  Chirality :  0.037   0.302   1360
  Planarity :  0.004   0.051   1093
  Dihedral  : 19.177 179.906   2291
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.37 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.31), residues: 697
  helix:  1.50 (0.24), residues: 462
  sheet: -0.93 (1.04), residues: 22
  loop : -0.25 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 619 
 TYR   0.034   0.001   TYR D 685 
 PHE   0.023   0.002   PHE D 691 
 TRP   0.006   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 8050)
  covalent geometry    : angle       0.53659 /  0.30 (11307)
  hydrogen bonds       : bond        0.05624 /  3.70 (  464)
  hydrogen bonds       : angle       4.30745 /  3.26 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7914 (tp30) cc_final: 0.7346 (tp30)
REVERT: C  132 GLN cc_start: 0.7550 (mt0) cc_final: 0.7110 (mp10)
REVERT: D    4 MET cc_start: 0.6998 (tpt) cc_final: 0.6173 (tpp)
REVERT: D  109 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7828 (tt)
REVERT: D  586 PHE cc_start: 0.5732 (m-80) cc_final: 0.5418 (m-80)
REVERT: D  743 MET cc_start: 0.8672 (tpt) cc_final: 0.8335 (tpt)
REVERT: D  780 SER cc_start: 0.8384 (m) cc_final: 0.8084 (p)
  outliers start: 18
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0671
  time to fit residues: 10.1896
Evaluate side-chains
  111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  531 THR
Chi-restraints excluded: chain D residue  588 PHE
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  806 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 32 optimal weight:    0.1980
   chunk 72 optimal weight:   10.0000
   chunk 77 optimal weight:   50.0000
   chunk 49 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 74 optimal weight:    9.9990
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 728 GLN
D 649 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.184420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.120850 restraints weight = 11911.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.09
r_work: 0.3303 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8050  Z= 0.121
  Angle     :  0.505   6.416  11307  Z= 0.284
  Chirality :  0.036   0.286   1360
  Planarity :  0.004   0.048   1093
  Dihedral  : 19.198 178.079   2291
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.53 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.31), residues: 697
  helix:  1.79 (0.24), residues: 461
  sheet: -0.87 (1.01), residues: 22
  loop : -0.22 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 724 
 TYR   0.036   0.001   TYR D 685 
 PHE   0.021   0.002   PHE C 147 
 TRP   0.006   0.001   TRP D 522 
 HIS   0.011   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 ( 8050)
  covalent geometry    : angle       0.50545 /  0.28 (11307)
  hydrogen bonds       : bond        0.05194 /  3.39 (  464)
  hydrogen bonds       : angle       4.13548 /  3.13 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7888 (tp30) cc_final: 0.7307 (tp30)
REVERT: A  728 GLN cc_start: 0.8171 (mt0) cc_final: 0.7966 (mt0)
REVERT: C   76 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7133 (pm20)
REVERT: C  132 GLN cc_start: 0.7595 (mt0) cc_final: 0.7145 (mp10)
REVERT: C  163 MET cc_start: 0.2633 (mmm) cc_final: 0.2127 (mmm)
REVERT: D    4 MET cc_start: 0.6919 (tpt) cc_final: 0.6092 (tpp)
REVERT: D  109 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7786 (tt)
REVERT: D  733 PHE cc_start: 0.7555 (t80) cc_final: 0.7324 (t80)
REVERT: D  743 MET cc_start: 0.8593 (tpt) cc_final: 0.8356 (tpt)
REVERT: D  755 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (mtpp)
REVERT: D  780 SER cc_start: 0.8401 (m) cc_final: 0.8165 (p)
  outliers start: 23
  outliers final: 14
  residues processed: 112
  average time/residue: 0.0696
  time to fit residues: 11.0347
Evaluate side-chains
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  565 ILE
Chi-restraints excluded: chain D residue  588 PHE
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  755 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 33 optimal weight:    0.0040
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.6194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 706 ASN
** D 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 620 ASN
D 624 ASN
D 649 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.184320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120908 restraints weight = 11943.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.10
r_work: 0.3306 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8050  Z= 0.117
  Angle     :  0.503   6.349  11307  Z= 0.280
  Chirality :  0.036   0.279   1360
  Planarity :  0.004   0.048   1093
  Dihedral  : 19.211 176.872   2291
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.36 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.32), residues: 697
  helix:  1.91 (0.24), residues: 463
  sheet: -1.13 (0.99), residues: 25
  loop : -0.09 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  20 
 TYR   0.035   0.001   TYR D 685 
 PHE   0.022   0.002   PHE C 147 
 TRP   0.006   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.12 ( 8050)
  covalent geometry    : angle       0.50317 /  0.28 (11307)
  hydrogen bonds       : bond        0.05000 /  3.24 (  464)
  hydrogen bonds       : angle       4.04823 /  3.08 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7861 (tp30) cc_final: 0.7273 (tp30)
REVERT: A  728 GLN cc_start: 0.8145 (mt0) cc_final: 0.7900 (mt0)
REVERT: B  740 MET cc_start: 0.5479 (ppp) cc_final: 0.4591 (mmm)
REVERT: C  123 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7548 (tp)
REVERT: C  132 GLN cc_start: 0.7605 (mt0) cc_final: 0.7147 (mp10)
REVERT: C  163 MET cc_start: 0.2683 (mmm) cc_final: 0.2214 (mmm)
REVERT: D    4 MET cc_start: 0.6897 (tpt) cc_final: 0.6078 (tpp)
REVERT: D  109 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7772 (tt)
REVERT: D  163 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7838 (ttp)
REVERT: D  619 ARG cc_start: 0.7642 (ptt90) cc_final: 0.7328 (ptt180)
REVERT: D  780 SER cc_start: 0.8421 (m) cc_final: 0.8185 (p)
  outliers start: 19
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0672
  time to fit residues: 10.3406
Evaluate side-chains
  109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  588 PHE
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  649 GLN
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  806 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0870
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0060
   overall best weight:    0.4574

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 706 ASN
D 140 HIS
** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.125551 restraints weight = 11870.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.35
r_work: 0.3294 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8050  Z= 0.111
  Angle     :  0.501   9.277  11307  Z= 0.276
  Chirality :  0.035   0.275   1360
  Planarity :  0.003   0.047   1093
  Dihedral  : 19.220 176.183   2291
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.35 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.32), residues: 697
  helix:  1.94 (0.24), residues: 463
  sheet: -1.10 (1.02), residues: 25
  loop :  0.00 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 799 
 TYR   0.037   0.001   TYR D 685 
 PHE   0.021   0.002   PHE C 147 
 TRP   0.005   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.11 ( 8050)
  covalent geometry    : angle       0.50081 /  0.28 (11307)
  hydrogen bonds       : bond        0.04855 /  3.14 (  464)
  hydrogen bonds       : angle       4.01532 /  3.07 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7850 (tp30) cc_final: 0.7271 (tp30)
REVERT: A  728 GLN cc_start: 0.8211 (mt0) cc_final: 0.7958 (mt0)
REVERT: C   76 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7132 (pm20)
REVERT: C  132 GLN cc_start: 0.7638 (mt0) cc_final: 0.7179 (mp10)
REVERT: C  163 MET cc_start: 0.2750 (mmm) cc_final: 0.2284 (mmm)
REVERT: D    4 MET cc_start: 0.6923 (tpt) cc_final: 0.6118 (tpp)
REVERT: D  109 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7786 (tt)
REVERT: D  163 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7860 (ttp)
REVERT: D  733 PHE cc_start: 0.7523 (t80) cc_final: 0.7288 (t80)
REVERT: D  755 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8399 (tttp)
REVERT: D  780 SER cc_start: 0.8432 (m) cc_final: 0.8209 (p)
  outliers start: 17
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0670
  time to fit residues: 10.0105
Evaluate side-chains
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  588 PHE
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  725 ILE
Chi-restraints excluded: chain D residue  806 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    0.2980
   chunk 9 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 706 ASN
D 649 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.184233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.120987 restraints weight = 11921.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.06
r_work: 0.3306 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8050  Z= 0.119
  Angle     :  0.508   7.918  11307  Z= 0.276
  Chirality :  0.035   0.265   1360
  Planarity :  0.003   0.048   1093
  Dihedral  : 19.208 174.885   2290
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.87 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.51 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.31), residues: 697
  helix:  2.06 (0.24), residues: 461
  sheet: -1.10 (1.03), residues: 25
  loop :  0.03 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 799 
 TYR   0.037   0.001   TYR D 685 
 PHE   0.021   0.002   PHE C 147 
 TRP   0.006   0.001   TRP D 522 
 HIS   0.005   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 ( 8050)
  covalent geometry    : angle       0.50812 /  0.28 (11307)
  hydrogen bonds       : bond        0.04757 /  3.08 (  464)
  hydrogen bonds       : angle       4.01048 /  3.06 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7769 (tp30) cc_final: 0.7114 (tp30)
REVERT: A  728 GLN cc_start: 0.8163 (mt0) cc_final: 0.7898 (mt0)
REVERT: B  740 MET cc_start: 0.6672 (tmm) cc_final: 0.4911 (mmt)
REVERT: C  123 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7581 (tp)
REVERT: C  132 GLN cc_start: 0.7627 (mt0) cc_final: 0.7255 (mp10)
REVERT: D    4 MET cc_start: 0.6880 (tpt) cc_final: 0.6084 (tpp)
REVERT: D  109 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7720 (tt)
REVERT: D  163 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7837 (ttp)
REVERT: D  538 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7965 (pt0)
REVERT: D  733 PHE cc_start: 0.7479 (t80) cc_final: 0.7257 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0542
  time to fit residues: 8.5911
Evaluate side-chains
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  588 PHE
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  725 ILE
Chi-restraints excluded: chain D residue  750 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 10 optimal weight:    0.4980
   chunk 77 optimal weight:   50.0000
   chunk 68 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0010
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    0.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 724 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.184301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.124620 restraints weight = 11886.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.28
r_work: 0.3275 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8050  Z= 0.117
  Angle     :  0.496   6.967  11307  Z= 0.271
  Chirality :  0.035   0.260   1360
  Planarity :  0.003   0.051   1093
  Dihedral  : 19.200 174.162   2290
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.01 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.68 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.32), residues: 697
  helix:  2.13 (0.24), residues: 461
  sheet: -0.99 (1.03), residues: 25
  loop :  0.01 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 799 
 TYR   0.034   0.001   TYR D 685 
 PHE   0.021   0.002   PHE C 147 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.12 ( 8050)
  covalent geometry    : angle       0.49624 /  0.27 (11307)
  hydrogen bonds       : bond        0.04651 /  3.00 (  464)
  hydrogen bonds       : angle       4.00710 /  3.07 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7772 (tp30) cc_final: 0.7108 (tp30)
REVERT: A  728 GLN cc_start: 0.8232 (mt0) cc_final: 0.7960 (mt0)
REVERT: B  740 MET cc_start: 0.6590 (tmm) cc_final: 0.4729 (mmt)
REVERT: C  123 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7623 (tp)
REVERT: C  132 GLN cc_start: 0.7634 (mt0) cc_final: 0.7301 (mp10)
REVERT: D    4 MET cc_start: 0.6910 (tpt) cc_final: 0.6131 (tpp)
REVERT: D  109 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7738 (tt)
REVERT: D  538 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7990 (pt0)
  outliers start: 18
  outliers final: 12
  residues processed: 103
  average time/residue: 0.0546
  time to fit residues: 8.5499
Evaluate side-chains
  101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  588 PHE
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  666 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 33 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6138

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.124202 restraints weight = 11938.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.34
r_work: 0.3284 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8050  Z= 0.113
  Angle     :  0.496   7.010  11307  Z= 0.271
  Chirality :  0.034   0.253   1360
  Planarity :  0.003   0.051   1093
  Dihedral  : 19.168 173.519   2290
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.87 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.84 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.32), residues: 697
  helix:  2.18 (0.24), residues: 461
  sheet: -0.93 (1.01), residues: 25
  loop :  0.05 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 799 
 TYR   0.034   0.001   TYR D 685 
 PHE   0.020   0.002   PHE C 147 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 ( 8050)
  covalent geometry    : angle       0.49563 /  0.27 (11307)
  hydrogen bonds       : bond        0.04527 /  2.91 (  464)
  hydrogen bonds       : angle       3.97243 /  3.05 ( 1272)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7758 (tp30) cc_final: 0.7092 (tp30)
REVERT: A  728 GLN cc_start: 0.8234 (mt0) cc_final: 0.7969 (mt0)
REVERT: A  742 MET cc_start: 0.7325 (mmt) cc_final: 0.6755 (ppp)
REVERT: C  123 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7550 (tp)
REVERT: C  132 GLN cc_start: 0.7648 (mt0) cc_final: 0.7312 (mp10)
REVERT: C  163 MET cc_start: 0.2456 (mmm) cc_final: 0.2084 (mmm)
REVERT: D    4 MET cc_start: 0.6898 (tpt) cc_final: 0.6121 (tpp)
REVERT: D  538 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8029 (pt0)
  outliers start: 15
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0531
  time to fit residues: 7.9512
Evaluate side-chains
  101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  153 ASP
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  588 PHE
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  604 THR
Chi-restraints excluded: chain D residue  666 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 34 optimal weight:    0.1980
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    0.2980
   chunk 20 optimal weight:    8.9990
   chunk 76 optimal weight:   30.0000
   chunk 29 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0270
   chunk 15 optimal weight:    0.0570
   overall best weight:    0.2556

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 716 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.185902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126594 restraints weight = 11900.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.30
r_work: 0.3325 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8050  Z= 0.100
  Angle     :  0.485   6.934  11307  Z= 0.264
  Chirality :  0.033   0.244   1360
  Planarity :  0.003   0.050   1093
  Dihedral  : 19.141 173.115   2290
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.58 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.50 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.32), residues: 697
  helix:  2.20 (0.24), residues: 464
  sheet: -0.70 (1.00), residues: 25
  loop : -0.01 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  20 
 TYR   0.041   0.001   TYR D 685 
 PHE   0.042   0.002   PHE D 733 
 TRP   0.005   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00193 /  0.10 ( 8050)
  covalent geometry    : angle       0.48545 /  0.26 (11307)
  hydrogen bonds       : bond        0.04205 /  2.67 (  464)
  hydrogen bonds       : angle       3.88608 /  2.99 ( 1272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1780.07 seconds
wall clock time: 31 minutes 11.30 seconds (1871.30 seconds total)