Starting phenix.real_space_refine
on Sun Apr  5 03:31:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rwb_54306/04_2026/9rwb_54306.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rwb_54306/04_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rwb_54306/04_2026/9rwb_54306.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rwb_54306/04_2026/9rwb_54306.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rwb_54306/04_2026/9rwb_54306.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rwb_54306/04_2026/9rwb_54306.map"
  }
  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-2.1rc1-6017/lib/python3.9/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: 2.15, per 1000 atoms: 0.28
  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: 0.70
  Conformation dependent library (CDL) restraints added in 213.3 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: 1.11
  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: 1.41

  Time building geometry restraints manager: 0.93 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: 10292
        1.76 -     3.51: 906
        3.51 -     5.27: 85
        5.27 -     7.03: 20
        7.03 -     8.79: 4
  Bond angle restraints: 11307
  Sorted by residual:
  angle pdb=" O3'   A E  94 "
        pdb=" C3'   A E  94 "
        pdb=" C2'   A E  94 "
      ideal   model   delta    sigma   weight residual
     113.70  120.14   -6.44 1.50e+00 4.44e-01 1.84e+01
  angle pdb=" O3'   C E  38 "
        pdb=" C3'   C E  38 "
        pdb=" C2'   C E  38 "
      ideal   model   delta    sigma   weight residual
     109.50  115.49   -5.99 1.50e+00 4.44e-01 1.59e+01
  angle pdb=" C3'   C E  38 "
        pdb=" O3'   C E  38 "
        pdb=" P     U E  39 "
      ideal   model   delta    sigma   weight residual
     120.20  125.95   -5.75 1.50e+00 4.44e-01 1.47e+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 1.50e+00 4.44e-01 1.35e+01
  angle pdb=" C3'   A E  94 "
        pdb=" O3'   A E  94 "
        pdb=" P     G E  95 "
      ideal   model   delta    sigma   weight residual
     120.20  125.61   -5.41 1.50e+00 4.44e-01 1.30e+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: 1145
       0.082 -    0.164: 196
       0.164 -    0.246: 14
       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      2.46    2.18    0.28 2.00e-01 2.50e+01 1.94e+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:             3.220
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.960
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
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= 0.286
  Angle     :  1.035   8.786  11307  Z= 0.616
  Chirality :  0.062   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
  covalent geometry    : bond        0.00508 ( 8050)
  covalent geometry    : angle       1.03464 (11307)
  hydrogen bonds       : bond        0.11791 (  464)
  hydrogen bonds       : angle       6.38360 ( 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  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7914 (tp30) cc_final: 0.7469 (tp30)
REVERT: A  746 MET cc_start: 0.4753 (mtt) cc_final: 0.3994 (ttp)
REVERT: C  132 GLN cc_start: 0.7434 (mt0) cc_final: 0.7146 (mp10)
REVERT: D   47 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.7942 (ttt-90)
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: 0.7418 (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: 0.7365 (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: 0.8005 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.0849
  time to fit residues: 14.7707
Evaluate side-chains
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
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:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 706 ASN
C  98 GLN
C 106 ASN
** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 664 ASN
D 714 HIS
D 724 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.183432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.125805 restraints weight = 12012.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.19
r_work: 0.3282 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8050  Z= 0.160
  Angle     :  0.625   8.677  11307  Z= 0.328
  Chirality :  0.039   0.169   1360
  Planarity :  0.004   0.057   1093
  Dihedral  : 19.235 179.610   2291
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.73 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 11.40 %
    Favored  : 85.12 %
  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:  0.95 (0.31), residues: 697
  helix:  1.20 (0.24), residues: 459
  sheet: -0.96 (0.98), residues: 25
  loop : -0.26 (0.42), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  20 
 TYR   0.035   0.002   TYR D 685 
 PHE   0.022   0.002   PHE C 147 
 TRP   0.010   0.002   TRP D 522 
 HIS   0.009   0.002   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8050)
  covalent geometry    : angle       0.62461 (11307)
  hydrogen bonds       : bond        0.05242 (  464)
  hydrogen bonds       : angle       4.60569 ( 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
  133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7924 (tp30) cc_final: 0.7425 (tp30)
REVERT: A  714 GLU cc_start: 0.8296 (tp30) cc_final: 0.8078 (tp30)
REVERT: A  728 GLN cc_start: 0.8106 (mt0) cc_final: 0.7854 (mt0)
REVERT: C  123 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7812 (tp)
REVERT: C  132 GLN cc_start: 0.7465 (mt0) cc_final: 0.7035 (mp10)
REVERT: D  109 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7845 (tt)
REVERT: D  572 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7028 (tm-30)
REVERT: D  586 PHE cc_start: 0.5803 (m-80) cc_final: 0.5427 (m-80)
REVERT: D  608 HIS cc_start: 0.7635 (t70) cc_final: 0.7358 (t-90)
REVERT: D  620 ASN cc_start: 0.8135 (m110) cc_final: 0.7921 (t0)
REVERT: D  626 TYR cc_start: 0.8509 (t80) cc_final: 0.8261 (t80)
REVERT: D  650 GLU cc_start: 0.7880 (tt0) cc_final: 0.7628 (tm-30)
REVERT: D  743 MET cc_start: 0.8943 (tpt) cc_final: 0.8570 (tpt)
REVERT: D  780 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8173 (p)
REVERT: D  790 MET cc_start: 0.8264 (mmm) cc_final: 0.8058 (mmm)
  outliers start: 21
  outliers final: 10
  residues processed: 120
  average time/residue: 0.0721
  time to fit residues: 12.1582
Evaluate side-chains
  109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
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  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  602 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  806 VAL
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:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 50 optimal weight:    0.4980
   chunk 60 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4276 r_free = 0.4276 target = 0.184129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.124938 restraints weight = 11798.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.25
r_work: 0.3280 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8050  Z= 0.127
  Angle     :  0.540   6.529  11307  Z= 0.284
  Chirality :  0.035   0.150   1360
  Planarity :  0.004   0.053   1093
  Dihedral  : 19.188 175.512   2291
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.05 %
    Favored  : 83.31 %
  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:  1.51 (0.31), residues: 697
  helix:  1.62 (0.24), residues: 462
  sheet: -0.62 (0.99), residues: 25
  loop : -0.06 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 799 
 TYR   0.027   0.001   TYR D 685 
 PHE   0.030   0.002   PHE D 691 
 TRP   0.007   0.001   TRP D 522 
 HIS   0.005   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8050)
  covalent geometry    : angle       0.53966 (11307)
  hydrogen bonds       : bond        0.04567 (  464)
  hydrogen bonds       : angle       4.21179 ( 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
  121 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7897 (tp30) cc_final: 0.7270 (tp30)
REVERT: A  728 GLN cc_start: 0.8153 (mt0) cc_final: 0.7854 (mt0)
REVERT: A  739 GLU cc_start: 0.7770 (tt0) cc_final: 0.7445 (tt0)
REVERT: A  742 MET cc_start: 0.7310 (mmt) cc_final: 0.6728 (ppp)
REVERT: C   76 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7224 (pm20)
REVERT: C  132 GLN cc_start: 0.7569 (mt0) cc_final: 0.7164 (mp10)
REVERT: C  163 MET cc_start: 0.2670 (mmm) cc_final: 0.2228 (mmm)
REVERT: D  109 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7793 (tt)
REVERT: D  163 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7829 (ttp)
REVERT: D  572 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6987 (tm-30)
REVERT: D  620 ASN cc_start: 0.8085 (m110) cc_final: 0.7675 (t0)
REVERT: D  626 TYR cc_start: 0.8318 (t80) cc_final: 0.8080 (t80)
REVERT: D  631 ILE cc_start: 0.7505 (pt) cc_final: 0.7195 (tt)
REVERT: D  743 MET cc_start: 0.8881 (tpt) cc_final: 0.8516 (tpt)
  outliers start: 16
  outliers final: 8
  residues processed: 113
  average time/residue: 0.0767
  time to fit residues: 12.2305
Evaluate side-chains
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  165 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  109 LEU
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  649 GLN
Chi-restraints excluded: chain D residue  806 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0060
   chunk 21 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.184216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.124394 restraints weight = 12037.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.25
r_work: 0.3282 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8050  Z= 0.121
  Angle     :  0.516   6.469  11307  Z= 0.270
  Chirality :  0.034   0.141   1360
  Planarity :  0.004   0.054   1093
  Dihedral  : 19.174 172.732   2291
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.54 %
    Favored  : 81.16 %
  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:  1.77 (0.31), residues: 697
  helix:  1.86 (0.24), residues: 462
  sheet: -0.47 (1.03), residues: 25
  loop : -0.07 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  20 
 TYR   0.027   0.001   TYR D 685 
 PHE   0.021   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
  covalent geometry    : bond        0.00253 ( 8050)
  covalent geometry    : angle       0.51639 (11307)
  hydrogen bonds       : bond        0.04323 (  464)
  hydrogen bonds       : angle       4.05583 ( 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
  120 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7782 (tp30) cc_final: 0.7146 (tp30)
REVERT: A  728 GLN cc_start: 0.8166 (mt0) cc_final: 0.7874 (mt0)
REVERT: A  742 MET cc_start: 0.7398 (mmt) cc_final: 0.6729 (ppp)
REVERT: B  740 MET cc_start: 0.6386 (tmm) cc_final: 0.4820 (mmt)
REVERT: C  123 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7626 (tp)
REVERT: C  132 GLN cc_start: 0.7645 (mt0) cc_final: 0.7241 (mp10)
REVERT: C  163 MET cc_start: 0.2700 (mmm) cc_final: 0.2321 (mmm)
REVERT: D    4 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.5771 (tpt)
REVERT: D  109 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7792 (tt)
REVERT: D  572 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6863 (tm-30)
REVERT: D  620 ASN cc_start: 0.8216 (m110) cc_final: 0.7871 (t0)
REVERT: D  631 ILE cc_start: 0.7512 (pt) cc_final: 0.7192 (tt)
REVERT: D  681 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6701 (mp)
REVERT: D  743 MET cc_start: 0.8783 (tpt) cc_final: 0.8544 (tpt)
  outliers start: 20
  outliers final: 12
  residues processed: 113
  average time/residue: 0.0705
  time to fit residues: 11.4945
Evaluate side-chains
  111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue    4 MET
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  562 CYS
Chi-restraints excluded: chain D residue  565 ILE
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  681 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:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 77 optimal weight:   20.0000
   chunk 49 optimal weight:    0.0060
   chunk 54 optimal weight:    0.3980
   chunk 22 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 74 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
D 140 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.185345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.122436 restraints weight = 11869.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.05
r_work: 0.3330 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3119

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= 0.107
  Angle     :  0.498   7.047  11307  Z= 0.260
  Chirality :  0.033   0.143   1360
  Planarity :  0.003   0.050   1093
  Dihedral  : 19.123 171.115   2290
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.70 %
    Favored  : 80.83 %
  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:  2.12 (0.24), residues: 464
  sheet: -0.42 (1.05), residues: 25
  loop : -0.07 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  20 
 TYR   0.026   0.001   TYR D 685 
 PHE   0.022   0.002   PHE C 147 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.003   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 8050)
  covalent geometry    : angle       0.49790 (11307)
  hydrogen bonds       : bond        0.03950 (  464)
  hydrogen bonds       : angle       3.87738 ( 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
  119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7729 (tp30) cc_final: 0.7083 (tp30)
REVERT: A  728 GLN cc_start: 0.8130 (mt0) cc_final: 0.7844 (mt0)
REVERT: A  742 MET cc_start: 0.7240 (mmt) cc_final: 0.6763 (ppp)
REVERT: B  740 MET cc_start: 0.6493 (tmm) cc_final: 0.6105 (ppp)
REVERT: C  123 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7491 (tp)
REVERT: C  132 GLN cc_start: 0.7616 (mt0) cc_final: 0.7218 (mp10)
REVERT: C  163 MET cc_start: 0.2684 (mmm) cc_final: 0.2322 (mmm)
REVERT: D    4 MET cc_start: 0.6821 (tpt) cc_final: 0.6010 (tpp)
REVERT: D  572 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6925 (tm-30)
REVERT: D  620 ASN cc_start: 0.8174 (m110) cc_final: 0.7846 (t0)
REVERT: D  681 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6792 (mp)
REVERT: D  755 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8486 (tttp)
  outliers start: 21
  outliers final: 13
  residues processed: 113
  average time/residue: 0.0785
  time to fit residues: 12.3583
Evaluate side-chains
  107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain B residue  734 THR
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  109 LEU
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  562 CYS
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  681 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:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
B 706 ASN
C  48 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.183156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.119607 restraints weight = 11989.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.09
r_work: 0.3284 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8050  Z= 0.140
  Angle     :  0.523   6.786  11307  Z= 0.271
  Chirality :  0.034   0.176   1360
  Planarity :  0.003   0.052   1093
  Dihedral  : 19.070 170.567   2290
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 16.86 %
    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:  2.21 (0.31), residues: 697
  helix:  2.22 (0.24), residues: 454
  sheet: -0.53 (1.03), residues: 25
  loop :  0.15 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 799 
 TYR   0.029   0.001   TYR D 685 
 PHE   0.020   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
  covalent geometry    : bond        0.00307 ( 8050)
  covalent geometry    : angle       0.52309 (11307)
  hydrogen bonds       : bond        0.04193 (  464)
  hydrogen bonds       : angle       3.98318 ( 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
  119 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7733 (tp30) cc_final: 0.6923 (tp30)
REVERT: A  728 GLN cc_start: 0.8096 (mt0) cc_final: 0.7783 (mt0)
REVERT: A  742 MET cc_start: 0.7195 (mmt) cc_final: 0.6721 (ppp)
REVERT: B  740 MET cc_start: 0.6594 (tmm) cc_final: 0.6319 (ppp)
REVERT: C  123 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7446 (tp)
REVERT: C  132 GLN cc_start: 0.7644 (mt0) cc_final: 0.7303 (mp10)
REVERT: C  163 MET cc_start: 0.2676 (mmm) cc_final: 0.2283 (mmm)
REVERT: D    4 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.5749 (tpt)
REVERT: D  538 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8021 (pt0)
REVERT: D  572 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6874 (tm-30)
REVERT: D  681 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6773 (mp)
REVERT: D  743 MET cc_start: 0.8514 (tpt) cc_final: 0.7976 (tpt)
REVERT: D  755 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8469 (tttp)
  outliers start: 22
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0735
  time to fit residues: 11.9579
Evaluate side-chains
  111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain B residue  734 THR
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    4 MET
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  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  636 VAL
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  681 LEU
Chi-restraints excluded: chain D residue  755 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0370
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
B 706 ASN
D 664 ASN
D 716 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.185301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.126654 restraints weight = 11886.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.36
r_work: 0.3312 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8050  Z= 0.105
  Angle     :  0.492   6.970  11307  Z= 0.256
  Chirality :  0.033   0.176   1360
  Planarity :  0.003   0.049   1093
  Dihedral  : 19.008 170.255   2290
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.87 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.19 %
    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:  2.27 (0.32), residues: 697
  helix:  2.27 (0.24), residues: 463
  sheet: -0.42 (1.01), residues: 25
  loop :  0.06 (0.41), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  20 
 TYR   0.033   0.001   TYR D 685 
 PHE   0.010   0.001   PHE D 637 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.004   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 8050)
  covalent geometry    : angle       0.49224 (11307)
  hydrogen bonds       : bond        0.03772 (  464)
  hydrogen bonds       : angle       3.86286 ( 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
  116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7751 (tp30) cc_final: 0.6971 (tp30)
REVERT: A  728 GLN cc_start: 0.8170 (mt0) cc_final: 0.7891 (mt0)
REVERT: A  742 MET cc_start: 0.7289 (mmt) cc_final: 0.6796 (ppp)
REVERT: C  123 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7507 (tp)
REVERT: C  132 GLN cc_start: 0.7735 (mt0) cc_final: 0.7384 (mp10)
REVERT: C  163 MET cc_start: 0.2755 (mmm) cc_final: 0.2386 (mmm)
REVERT: D    4 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6089 (tpp)
REVERT: D  149 MET cc_start: 0.8027 (mmt) cc_final: 0.7815 (mmm)
REVERT: D  538 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8009 (pt0)
REVERT: D  572 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6884 (tm-30)
REVERT: D  646 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8009 (mt)
REVERT: D  685 TYR cc_start: 0.7210 (m-80) cc_final: 0.6959 (m-80)
REVERT: D  743 MET cc_start: 0.8501 (tpt) cc_final: 0.7978 (tpt)
REVERT: D  755 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8566 (tttp)
  outliers start: 20
  outliers final: 10
  residues processed: 112
  average time/residue: 0.0827
  time to fit residues: 12.8402
Evaluate side-chains
  106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  734 THR
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    4 MET
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  646 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  755 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 34 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0170
   chunk 44 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
B 706 ASN
D 683 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.184809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.125240 restraints weight = 11984.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.31
r_work: 0.3302 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8050  Z= 0.113
  Angle     :  0.497   6.862  11307  Z= 0.258
  Chirality :  0.034   0.292   1360
  Planarity :  0.003   0.050   1093
  Dihedral  : 18.953 169.919   2290
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.87 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.02 %
    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:  2.33 (0.32), residues: 697
  helix:  2.31 (0.24), residues: 461
  sheet: -0.41 (0.99), residues: 25
  loop :  0.12 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 736 
 TYR   0.034   0.001   TYR D 685 
 PHE   0.034   0.002   PHE D 691 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.002   0.000   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8050)
  covalent geometry    : angle       0.49724 (11307)
  hydrogen bonds       : bond        0.03798 (  464)
  hydrogen bonds       : angle       3.83829 ( 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
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  710 GLU cc_start: 0.7784 (tp30) cc_final: 0.7259 (tp30)
REVERT: A  728 GLN cc_start: 0.8129 (mt0) cc_final: 0.7832 (mt0)
REVERT: A  742 MET cc_start: 0.7285 (mmt) cc_final: 0.6753 (ppp)
REVERT: B  740 MET cc_start: 0.6621 (tmm) cc_final: 0.4723 (mmt)
REVERT: C  123 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7507 (tp)
REVERT: C  132 GLN cc_start: 0.7700 (mt0) cc_final: 0.7335 (mp10)
REVERT: C  163 MET cc_start: 0.2544 (mmm) cc_final: 0.2279 (mmm)
REVERT: D    4 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6062 (tpp)
REVERT: D  538 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8038 (pt0)
REVERT: D  572 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6916 (tm-30)
REVERT: D  685 TYR cc_start: 0.7200 (m-80) cc_final: 0.6947 (m-80)
REVERT: D  743 MET cc_start: 0.8536 (tpt) cc_final: 0.7997 (tpt)
REVERT: D  755 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8566 (tttp)
  outliers start: 20
  outliers final: 12
  residues processed: 107
  average time/residue: 0.0783
  time to fit residues: 11.9199
Evaluate side-chains
  107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue    4 MET
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  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  565 ILE
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  755 LYS
Chi-restraints excluded: chain D residue  786 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 706 ASN
D 724 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.180512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116776 restraints weight = 11829.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.03
r_work: 0.3251 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8050  Z= 0.198
  Angle     :  0.584   6.761  11307  Z= 0.300
  Chirality :  0.037   0.295   1360
  Planarity :  0.004   0.059   1093
  Dihedral  : 18.988 169.692   2290
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.16 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.69 %
    Favored  : 79.17 %
  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:  2.02 (0.31), residues: 697
  helix:  2.07 (0.24), residues: 455
  sheet: -0.55 (1.01), residues: 25
  loop :  0.08 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 736 
 TYR   0.033   0.002   TYR D 685 
 PHE   0.032   0.002   PHE D 691 
 TRP   0.005   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 8050)
  covalent geometry    : angle       0.58390 (11307)
  hydrogen bonds       : bond        0.04638 (  464)
  hydrogen bonds       : angle       4.15007 ( 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
  112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7724 (tp30) cc_final: 0.7140 (tp30)
REVERT: B  740 MET cc_start: 0.6715 (tmm) cc_final: 0.5908 (ppp)
REVERT: C  123 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7532 (tp)
REVERT: C  132 GLN cc_start: 0.7592 (mt0) cc_final: 0.7332 (mp10)
REVERT: D   41 GLU cc_start: 0.7943 (tt0) cc_final: 0.7691 (tt0)
REVERT: D  538 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8020 (pt0)
REVERT: D  572 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6749 (tm-30)
  outliers start: 19
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0691
  time to fit residues: 10.8308
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  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain B residue  734 THR
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  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  565 ILE
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  598 THR
Chi-restraints excluded: chain D residue  636 VAL
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  786 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:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0000
   chunk 43 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
B 706 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.183776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.120638 restraints weight = 11867.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.07
r_work: 0.3305 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8050  Z= 0.119
  Angle     :  0.525   6.917  11307  Z= 0.271
  Chirality :  0.034   0.270   1360
  Planarity :  0.003   0.054   1093
  Dihedral  : 18.968 169.572   2290
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.16 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 18.35 %
    Favored  : 79.01 %
  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 (0.31), residues: 697
  helix:  2.21 (0.24), residues: 459
  sheet: -0.43 (1.01), residues: 25
  loop : -0.01 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 736 
 TYR   0.035   0.001   TYR D 685 
 PHE   0.030   0.002   PHE D 691 
 TRP   0.003   0.000   TRP D 522 
 HIS   0.012   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8050)
  covalent geometry    : angle       0.52459 (11307)
  hydrogen bonds       : bond        0.04023 (  464)
  hydrogen bonds       : angle       3.94123 ( 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
  108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  710 GLU cc_start: 0.7786 (tp30) cc_final: 0.7111 (tp30)
REVERT: A  728 GLN cc_start: 0.8112 (mt0) cc_final: 0.7799 (mt0)
REVERT: B  740 MET cc_start: 0.6588 (tmm) cc_final: 0.5740 (ppp)
REVERT: C  123 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7549 (tp)
REVERT: C  132 GLN cc_start: 0.7615 (mt0) cc_final: 0.7279 (mp10)
REVERT: D  149 MET cc_start: 0.7970 (mmt) cc_final: 0.7747 (mmm)
REVERT: D  572 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6757 (tm-30)
REVERT: D  577 GLU cc_start: 0.7807 (pp20) cc_final: 0.7316 (pp20)
REVERT: D  743 MET cc_start: 0.8465 (tpt) cc_final: 0.7949 (tpt)
  outliers start: 16
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0758
  time to fit residues: 11.3388
Evaluate side-chains
  103 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain C residue   76 GLN
Chi-restraints excluded: chain C residue  123 LEU
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  527 LEU
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  565 ILE
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain D residue  593 CYS
Chi-restraints excluded: chain D residue  598 THR
Chi-restraints excluded: chain D residue  786 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0970
   chunk 20 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0770
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
D 643 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.184395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.121601 restraints weight = 11814.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.03
r_work: 0.3319 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8050  Z= 0.114
  Angle     :  0.522   6.979  11307  Z= 0.269
  Chirality :  0.033   0.257   1360
  Planarity :  0.003   0.054   1093
  Dihedral  : 18.965 169.622   2290
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.16 %
    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:  2.26 (0.32), residues: 697
  helix:  2.25 (0.24), residues: 461
  sheet: -0.47 (0.97), residues: 25
  loop :  0.11 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 736 
 TYR   0.011   0.001   TYR D 648 
 PHE   0.033   0.002   PHE D 691 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.010   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8050)
  covalent geometry    : angle       0.52246 (11307)
  hydrogen bonds       : bond        0.03870 (  464)
  hydrogen bonds       : angle       3.91375 ( 1272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2088.06 seconds
wall clock time: 36 minutes 31.48 seconds (2191.48 seconds total)