Starting phenix.real_space_refine
on Sun Apr  5 03:31:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw6_54300/04_2026/9rw6_54300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw6_54300/04_2026/9rw6_54300.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/9rw6_54300/04_2026/9rw6_54300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw6_54300/04_2026/9rw6_54300.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw6_54300/04_2026/9rw6_54300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw6_54300/04_2026/9rw6_54300.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=   0.014
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     116      5.49       5
     S      29      5.16       5
     C    4469      2.51       5
     N    1331      2.21       5
     O    1815      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 7760
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 351
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'TRANS': 48}
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 347
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'TRANS': 48}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 50
    Chain: "E"
      Number of atoms: 1218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1218
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 22, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 6, 'rna3p': 51}
    Chain: "D"
      Number of atoms: 3440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3440
          Classifications: {'peptide': 452}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 10, 'TRANS': 441}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 211
          Unresolved non-hydrogen angles: 251
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 5, 'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 124
    Chain: "C"
      Number of atoms: 1186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1186
          Classifications: {'peptide': 152}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 147}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 46
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "F"
      Number of atoms: 1218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1218
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 22, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 6, 'rna3p': 51}
  Time building chain proxies: 1.96, per 1000 atoms: 0.25
  Number of scatterers: 7760
  At special positions: 0
  Unit cell: (88.956, 90.015, 152.496, 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      29     16.00
     P     116     15.00
     O    1815      8.00
     N    1331      7.00
     C    4469      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: 0.60
  Conformation dependent library (CDL) restraints added in 209.5 milliseconds
  

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1338

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      71.7% alpha, 7.5% beta
      44 base pairs and 58 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 698 through 745
      removed outlier: 3.761A  pdb=" N   GLU A 745 " --> pdb=" O   GLU A 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 698 through 744
    Processing helix  chain 'D' and resid 5 through 25
    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 50
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 112
      removed outlier: 3.565A  pdb=" N   GLU D  99 " --> pdb=" O   ASP D  95 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS D 107 " --> pdb=" O   TYR D 103 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LEU D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN D 110 " --> pdb=" O   ASN D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 126
      removed outlier: 3.955A  pdb=" N   GLY D 124 " --> pdb=" O   ARG D 120 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG D 126 " --> pdb=" O   LEU D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 129
      No H-bonds generated for 'chain 'D' and resid 127 through 129'
    Processing helix  chain 'D' and resid 132 through 137
    Processing helix  chain 'D' and resid 140 through 152
    Processing helix  chain 'D' and resid 521 through 528
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 593 through 600
      removed outlier: 4.248A  pdb=" N   VAL D 597 " --> pdb=" O   CYS D 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 618 through 629
    Processing helix  chain 'D' and resid 639 through 651
    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: 3.554A  pdb=" N   GLN D 680 " --> pdb=" O   PRO D 676 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ILE D 684 " --> pdb=" O   GLN D 680 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 689 through 692
      removed outlier: 3.715A  pdb=" N   TRP D 692 " --> pdb=" O   GLN D 689 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 689 through 692'
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 3.664A  pdb=" N   MET D 702 " --> pdb=" O   THR D 698 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA D 705 " --> pdb=" O   MET D 701 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 714 through 725
      removed outlier: 3.853A  pdb=" N   ASN D 720 " --> pdb=" O   GLN D 716 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 726 through 744
      removed outlier: 4.046A  pdb=" N   LEU D 732 " --> pdb=" O   GLU D 728 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLN D 744 " --> pdb=" O   GLN D 740 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.789A  pdb=" N   ASP D 765 " --> pdb=" O   THR D 761 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 790
      removed outlier: 4.235A  pdb=" N   TYR D 789 " --> pdb=" O   ARG D 785 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 793 through 801
    Processing helix  chain 'D' and resid 803 through 816
      removed outlier: 3.637A  pdb=" N   LYS D 809 " --> pdb=" O   LYS D 805 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 25
      removed outlier: 3.528A  pdb=" N   THR C  13 " --> pdb=" O   ALA C   9 " (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 51
    Processing helix  chain 'C' and resid 53 through 64
      removed outlier: 3.980A  pdb=" N   TYR C  64 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 112
      removed outlier: 3.870A  pdb=" N   GLU C  99 " --> pdb=" O   ASP C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 126
      removed outlier: 3.679A  pdb=" N   LEU C 123 " --> pdb=" O   VAL C 119 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ARG C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 119 through 126'
    Processing helix  chain 'C' and resid 130 through 137
      removed outlier: 3.685A  pdb=" N   ILE C 136 " --> pdb=" O   GLN C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 152
      removed outlier: 3.776A  pdb=" N   LEU C 148 " --> pdb=" O   PHE C 144 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   MET C 149 " --> pdb=" O   THR C 145 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   HIS C 151 " --> pdb=" O   PHE C 147 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'D' and resid 155 through 158
    Processing sheet with id=AA3, first strand: chain 'D' and resid 530 through 533
      removed outlier: 5.335A  pdb=" N   ILE D 573 " --> pdb=" O   ILE D 565 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ILE D 565 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU D 575 " --> pdb=" O   GLU D 563 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLU D 563 " --> pdb=" O   LEU D 575 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ILE D 556 " --> pdb=" O   ILE D 612 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   VAL D 614 " --> pdb=" O   ILE D 556 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   VAL D 558 " --> pdb=" O   VAL D 614 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   PHE D 637 " --> pdb=" O   VAL D 611 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158

    355 hydrogen bonds defined for protein.
    1035 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      112 hydrogen bonds
      220 hydrogen bond angles
      0 basepair planarities
      44 basepair parallelities
      58 stacking parallelities
  Total time for adding SS restraints: 1.30

  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:
        1.15 -     1.28: 1036
        1.28 -     1.41: 2257
        1.41 -     1.55: 4534
        1.55 -     1.68: 236
        1.68 -     1.81: 49
  Bond restraints: 8112
  Sorted by residual:
  bond pdb=" CA  LEU B 733 "
       pdb=" C   LEU B 733 "
    ideal  model  delta    sigma   weight residual
    1.524  1.392  0.132 1.26e-02 6.30e+03 1.10e+02
  bond pdb=" CA  ARG B 736 "
       pdb=" C   ARG B 736 "
    ideal  model  delta    sigma   weight residual
    1.524  1.406  0.117 1.37e-02 5.33e+03 7.33e+01
  bond pdb=" C   LEU B 733 "
       pdb=" O   LEU B 733 "
    ideal  model  delta    sigma   weight residual
    1.237  1.149  0.088 1.16e-02 7.43e+03 5.70e+01
  bond pdb=" C   ARG C  10 "
       pdb=" O   ARG C  10 "
    ideal  model  delta    sigma   weight residual
    1.237  1.155  0.081 1.17e-02 7.31e+03 4.83e+01
  bond pdb=" CA  ARG C 120 "
       pdb=" C   ARG C 120 "
    ideal  model  delta    sigma   weight residual
    1.523  1.437  0.086 1.30e-02 5.92e+03 4.36e+01
  ... (remaining 8107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 11431
        2.99 -     5.97: 73
        5.97 -     8.96: 6
        8.96 -    11.95: 0
       11.95 -    14.94: 1
  Bond angle restraints: 11511
  Sorted by residual:
  angle pdb=" O3'   U E  40 "
        pdb=" C3'   U E  40 "
        pdb=" C2'   U E  40 "
      ideal   model   delta    sigma   weight residual
     109.50   94.56   14.94 1.50e+00 4.44e-01 9.92e+01
  angle pdb=" N   LEU B 733 "
        pdb=" CA  LEU B 733 "
        pdb=" C   LEU B 733 "
      ideal   model   delta    sigma   weight residual
     111.14  103.32    7.82 1.08e+00 8.57e-01 5.25e+01
  angle pdb=" O   VAL C 119 "
        pdb=" C   VAL C 119 "
        pdb=" N   ARG C 120 "
      ideal   model   delta    sigma   weight residual
     122.57  114.40    8.17 1.25e+00 6.40e-01 4.27e+01
  angle pdb=" CA  VAL C 119 "
        pdb=" C   VAL C 119 "
        pdb=" N   ARG C 120 "
      ideal   model   delta    sigma   weight residual
     116.60  125.31   -8.71 1.45e+00 4.76e-01 3.61e+01
  angle pdb=" C4'   U E  40 "
        pdb=" C3'   U E  40 "
        pdb=" O3'   U E  40 "
      ideal   model   delta    sigma   weight residual
     109.40  117.77   -8.37 1.50e+00 4.44e-01 3.11e+01
  ... (remaining 11506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.68: 4454
       24.68 -    49.35: 422
       49.35 -    74.03: 212
       74.03 -    98.71: 7
       98.71 -   123.38: 1
  Dihedral angle restraints: 5096
    sinusoidal: 3037
      harmonic: 2059
  Sorted by residual:
  dihedral pdb=" O4'   U E  40 "
           pdb=" C4'   U E  40 "
           pdb=" C3'   U E  40 "
           pdb=" C2'   U E  40 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -15.06   39.06     1      8.00e+00 1.56e-02 3.35e+01
  dihedral pdb=" C3'   U E  40 "
           pdb=" C4'   U E  40 "
           pdb=" O4'   U E  40 "
           pdb=" C1'   U E  40 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   33.30  -35.30     1      8.00e+00 1.56e-02 2.76e+01
  dihedral pdb=" O4'   U F  27 "
           pdb=" C1'   U F  27 "
           pdb=" N1    U F  27 "
           pdb=" C2    U F  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -97.94  -62.06     1      1.50e+01 4.44e-03 2.27e+01
  ... (remaining 5093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1266
       0.043 -    0.086: 124
       0.086 -    0.130: 39
       0.130 -    0.173: 1
       0.173 -    0.216: 3
  Chirality restraints: 1433
  Sorted by residual:
  chirality pdb=" C2'   U E  40 "
            pdb=" C3'   U E  40 "
            pdb=" O2'   U E  40 "
            pdb=" C1'   U E  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.73    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ARG C 120 "
            pdb=" N   ARG C 120 "
            pdb=" C   ARG C 120 "
            pdb=" CB  ARG C 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  ASP D 159 "
            pdb=" N   ASP D 159 "
            pdb=" C   ASP D 159 "
            pdb=" CB  ASP D 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  ... (remaining 1430 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 735 "   -0.022 2.00e-02 2.50e+03   4.33e-02 1.87e+01
        pdb=" C   GLN B 735 "    0.075 2.00e-02 2.50e+03
        pdb=" O   GLN B 735 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ARG B 736 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 732 "    0.014 2.00e-02 2.50e+03   2.64e-02 6.97e+00
        pdb=" C   ALA B 732 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ALA B 732 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B 733 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 736 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.06e+00
        pdb=" C   ARG B 736 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ARG B 736 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU B 737 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 148
        2.63 -     3.20: 7536
        3.20 -     3.76: 13422
        3.76 -     4.33: 17497
        4.33 -     4.90: 25911
  Nonbonded interactions: 64514
  Sorted by model distance:
  nonbonded pdb=" O2'   U F  20 "
            pdb=" O2    U F  39 "
     model   vdw
     2.061 3.040
  nonbonded pdb=" O   MET D 149 "
            pdb=" OG1 THR D 152 "
     model   vdw
     2.081 3.040
  nonbonded pdb=" O   LYS D 775 "
            pdb=" OH  TYR D 803 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" O3'   U E  40 "
            pdb=" O2'   U E  40 "
     model   vdw
     2.128 2.432
  nonbonded pdb=" OE1 GLN C 128 "
            pdb=" O2'   U F  23 "
     model   vdw
     2.249 3.040
  ... (remaining 64509 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 697 through 712 or (resid 713 through 714 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 715 through 737 or (resid 738  \ 
through 739 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 
0 through 745))
  selection = (chain 'B' and (resid 697 through 713 or (resid 714 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 715 through 745))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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:             2.950
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.920
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
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   0.132   8112  Z= 0.310
  Angle     :  0.592  14.937  11511  Z= 0.354
  Chirality :  0.032   0.216   1433
  Planarity :  0.003   0.043   1056
  Dihedral  : 20.789 123.384   3758
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.36 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 17.49 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.33), residues: 688
  helix:  1.66 (0.25), residues: 443
  sheet: -0.16 (0.92), residues: 32
  loop : -0.34 (0.45), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  10 
 TYR   0.013   0.001   TYR C  64 
 PHE   0.009   0.001   PHE D  17 
 TRP   0.001   0.000   TRP D 692 
 HIS   0.002   0.000   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8112)
  covalent geometry    : angle       0.59155 (11511)
  hydrogen bonds       : bond        0.21332 (  467)
  hydrogen bonds       : angle       6.70570 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: B  708 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8562 (mm-40)
REVERT: D  586 PHE cc_start: 0.8006 (m-80) cc_final: 0.7686 (m-80)
REVERT: C  144 PHE cc_start: 0.7799 (t80) cc_final: 0.7330 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 110
  average time/residue: 0.1166
  time to fit residues: 16.4948
Evaluate side-chains
  86 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  560 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
D 538 GLN
D 624 ASN
C 151 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.146620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.111829 restraints weight = 18405.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 4.09
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8112  Z= 0.172
  Angle     :  0.600   7.956  11511  Z= 0.313
  Chirality :  0.036   0.162   1433
  Planarity :  0.004   0.033   1056
  Dihedral  : 20.614 135.587   2563
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  3.63 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.44 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.32), residues: 688
  helix:  1.87 (0.24), residues: 459
  sheet: -0.80 (0.83), residues: 33
  loop : -0.52 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 699 
 TYR   0.017   0.002   TYR D 685 
 PHE   0.014   0.002   PHE D  17 
 TRP   0.012   0.003   TRP D 692 
 HIS   0.009   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8112)
  covalent geometry    : angle       0.59988 (11511)
  hydrogen bonds       : bond        0.05145 (  467)
  hydrogen bonds       : angle       4.67803 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8037 (ttpt)
REVERT: D  742 LEU cc_start: 0.8173 (mm) cc_final: 0.7918 (tp)
REVERT: C  144 PHE cc_start: 0.7491 (t80) cc_final: 0.7220 (t80)
  outliers start: 14
  outliers final: 6
  residues processed: 102
  average time/residue: 0.1250
  time to fit residues: 16.1061
Evaluate side-chains
  88 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0970
   chunk 2 optimal weight:    0.5980
   chunk 73 optimal weight:    9.9990
   chunk 57 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0040
   chunk 26 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.3990

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

Flipped N/Q/H residues before XYZ refinement:
D 106 ASN
D 669 GLN
D 740 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.148432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.104836 restraints weight = 18232.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.34
r_work: 0.3477 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8112  Z= 0.123
  Angle     :  0.539   7.940  11511  Z= 0.278
  Chirality :  0.033   0.181   1433
  Planarity :  0.004   0.082   1056
  Dihedral  : 20.356 125.664   2561
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.77 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.33), residues: 688
  helix:  2.03 (0.25), residues: 458
  sheet: -0.50 (0.82), residues: 32
  loop : -0.38 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.018   0.001   TYR D 685 
 PHE   0.016   0.002   PHE D 718 
 TRP   0.014   0.004   TRP D 692 
 HIS   0.004   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8112)
  covalent geometry    : angle       0.53909 (11511)
  hydrogen bonds       : bond        0.04223 (  467)
  hydrogen bonds       : angle       4.26399 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  716 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8358 (ttpt)
REVERT: B  717 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7446 (ttmt)
REVERT: D  742 LEU cc_start: 0.8996 (mm) cc_final: 0.8664 (tp)
REVERT: C   80 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.6604 (t80)
  outliers start: 19
  outliers final: 7
  residues processed: 109
  average time/residue: 0.1087
  time to fit residues: 15.3673
Evaluate side-chains
  90 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain B residue  717 LYS
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:   20.0000
   chunk 44 optimal weight:    0.5980
   chunk 19 optimal weight:    0.1980
   chunk 68 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.147567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.103127 restraints weight = 18311.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.57
r_work: 0.3442 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8112  Z= 0.143
  Angle     :  0.559   7.771  11511  Z= 0.286
  Chirality :  0.034   0.168   1433
  Planarity :  0.004   0.044   1056
  Dihedral  : 20.254 114.452   2561
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 17.68 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.33), residues: 688
  helix:  1.98 (0.25), residues: 457
  sheet: -0.43 (0.83), residues: 32
  loop : -0.29 (0.45), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 757 
 TYR   0.020   0.001   TYR D 685 
 PHE   0.024   0.002   PHE C 144 
 TRP   0.002   0.001   TRP D 692 
 HIS   0.002   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8112)
  covalent geometry    : angle       0.55873 (11511)
  hydrogen bonds       : bond        0.04223 (  467)
  hydrogen bonds       : angle       4.09752 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  716 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8364 (ttpt)
REVERT: D   42 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7144 (m-80)
REVERT: D  146 ASP cc_start: 0.8423 (t0) cc_final: 0.8180 (t0)
REVERT: D  618 CYS cc_start: 0.9124 (t) cc_final: 0.8811 (t)
REVERT: D  692 TRP cc_start: 0.7002 (OUTLIER) cc_final: 0.6034 (m100)
REVERT: D  701 MET cc_start: 0.6475 (mtp) cc_final: 0.6250 (mtp)
REVERT: D  790 MET cc_start: 0.7977 (tmm) cc_final: 0.7489 (tmm)
REVERT: C  119 VAL cc_start: 0.6092 (OUTLIER) cc_final: 0.5778 (p)
  outliers start: 26
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1180
  time to fit residues: 16.3848
Evaluate side-chains
  96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  692 TRP
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 43 optimal weight:    8.9990
   chunk 59 optimal weight:    0.0970
   chunk 9 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8178

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

Flipped N/Q/H residues before XYZ refinement:
D 125 HIS
C 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.146925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.112745 restraints weight = 18168.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 4.27
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
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      :  0.004   0.090   8112  Z= 0.159
  Angle     :  0.567   8.009  11511  Z= 0.289
  Chirality :  0.035   0.154   1433
  Planarity :  0.004   0.051   1056
  Dihedral  : 20.275 113.390   2561
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.22 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 18.63 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.33), residues: 688
  helix:  1.98 (0.24), residues: 459
  sheet: -0.50 (0.82), residues: 32
  loop : -0.31 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 120 
 TYR   0.018   0.001   TYR D 685 
 PHE   0.023   0.002   PHE C 144 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.002   0.001   HIS C 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8112)
  covalent geometry    : angle       0.56742 (11511)
  hydrogen bonds       : bond        0.04275 (  467)
  hydrogen bonds       : angle       4.06614 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: A  716 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8041 (ttpt)
REVERT: D   42 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.6588 (m-80)
REVERT: D  146 ASP cc_start: 0.7660 (t0) cc_final: 0.7414 (t0)
REVERT: D  692 TRP cc_start: 0.6300 (OUTLIER) cc_final: 0.6082 (m100)
REVERT: C  105 LYS cc_start: 0.7809 (tptt) cc_final: 0.7413 (tptt)
REVERT: C  109 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7802 (pp)
  outliers start: 22
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1144
  time to fit residues: 15.2357
Evaluate side-chains
  95 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  692 TRP
Chi-restraints excluded: chain D residue  739 GLU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.147308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.112961 restraints weight = 18207.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 4.28
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   8112  Z= 0.143
  Angle     :  0.562   9.094  11511  Z= 0.282
  Chirality :  0.034   0.169   1433
  Planarity :  0.004   0.042   1056
  Dihedral  : 20.254 112.125   2561
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.78 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.72 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.33), residues: 688
  helix:  1.97 (0.25), residues: 459
  sheet: -0.42 (0.84), residues: 32
  loop : -0.29 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 120 
 TYR   0.022   0.001   TYR D 549 
 PHE   0.028   0.002   PHE D 718 
 TRP   0.002   0.001   TRP D 692 
 HIS   0.001   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8112)
  covalent geometry    : angle       0.56221 (11511)
  hydrogen bonds       : bond        0.04111 (  467)
  hydrogen bonds       : angle       4.04148 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  709 LEU cc_start: 0.8477 (tt) cc_final: 0.7953 (tp)
REVERT: A  713 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7970 (tm-30)
REVERT: A  716 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8008 (ttpt)
REVERT: D   42 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.6606 (m-80)
REVERT: D  146 ASP cc_start: 0.7558 (t0) cc_final: 0.7318 (t0)
REVERT: C  109 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7690 (pp)
  outliers start: 19
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1041
  time to fit residues: 13.4141
Evaluate side-chains
  95 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  739 GLU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  130 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0870
   chunk 8 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 41 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.147733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.101642 restraints weight = 18242.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.06
r_work: 0.3486 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8112  Z= 0.136
  Angle     :  0.557   7.605  11511  Z= 0.280
  Chirality :  0.033   0.146   1433
  Planarity :  0.004   0.037   1056
  Dihedral  : 20.237 111.921   2561
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.78 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 20.15 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.33), residues: 688
  helix:  2.07 (0.25), residues: 455
  sheet: -0.48 (0.86), residues: 32
  loop : -0.31 (0.45), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 120 
 TYR   0.020   0.001   TYR D 685 
 PHE   0.020   0.002   PHE C 144 
 TRP   0.016   0.003   TRP D 692 
 HIS   0.002   0.001   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8112)
  covalent geometry    : angle       0.55656 (11511)
  hydrogen bonds       : bond        0.04011 (  467)
  hydrogen bonds       : angle       3.91553 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: A  716 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8335 (ttpt)
REVERT: D   42 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7062 (m-80)
REVERT: D  132 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8024 (mp10)
REVERT: D  146 ASP cc_start: 0.8328 (t0) cc_final: 0.8116 (t0)
REVERT: D  608 HIS cc_start: 0.7354 (t-170) cc_final: 0.7047 (t70)
REVERT: D  618 CYS cc_start: 0.9111 (t) cc_final: 0.8713 (t)
REVERT: D  790 MET cc_start: 0.8296 (tmm) cc_final: 0.7535 (tmm)
REVERT: C   80 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.6691 (t80)
REVERT: C  105 LYS cc_start: 0.7903 (tptt) cc_final: 0.7488 (tptt)
REVERT: C  109 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8043 (pp)
  outliers start: 23
  outliers final: 13
  residues processed: 102
  average time/residue: 0.1136
  time to fit residues: 15.0286
Evaluate side-chains
  100 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  712 LEU
Chi-restraints excluded: chain D residue  739 GLU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  130 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 77 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0980
   chunk 37 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.5500

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.147535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.101602 restraints weight = 17826.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.04
r_work: 0.3461 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8112  Z= 0.130
  Angle     :  0.561   8.123  11511  Z= 0.280
  Chirality :  0.033   0.163   1433
  Planarity :  0.004   0.033   1056
  Dihedral  : 20.219 112.042   2561
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.92 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 20.15 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.33), residues: 688
  helix:  1.99 (0.25), residues: 465
  sheet: -0.84 (0.92), residues: 27
  loop : -0.37 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 753 
 TYR   0.022   0.001   TYR D 685 
 PHE   0.033   0.002   PHE D 718 
 TRP   0.014   0.003   TRP D 692 
 HIS   0.002   0.000   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8112)
  covalent geometry    : angle       0.56067 (11511)
  hydrogen bonds       : bond        0.03922 (  467)
  hydrogen bonds       : angle       3.85263 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8073 (tm-30)
REVERT: A  716 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8391 (ttpt)
REVERT: B  709 LEU cc_start: 0.9218 (tt) cc_final: 0.8927 (mm)
REVERT: D   42 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7166 (m-80)
REVERT: D  132 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7958 (mp10)
REVERT: D  134 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6881 (ptp-170)
REVERT: D  146 ASP cc_start: 0.8288 (t0) cc_final: 0.8065 (t0)
REVERT: D  608 HIS cc_start: 0.7346 (t-170) cc_final: 0.7017 (t70)
REVERT: D  618 CYS cc_start: 0.9070 (t) cc_final: 0.8726 (t)
REVERT: C   80 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.6710 (t80)
REVERT: C  109 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7936 (pp)
  outliers start: 23
  outliers final: 13
  residues processed: 98
  average time/residue: 0.0983
  time to fit residues: 12.8480
Evaluate side-chains
  100 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  712 LEU
Chi-restraints excluded: chain D residue  739 GLU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   46 MET
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  130 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0010
   chunk 66 optimal weight:    0.9990
   chunk 71 optimal weight:    0.1980
   overall best weight:    0.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.148533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.102673 restraints weight = 18135.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.06
r_work: 0.3479 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8112  Z= 0.117
  Angle     :  0.546   7.590  11511  Z= 0.274
  Chirality :  0.032   0.137   1433
  Planarity :  0.004   0.043   1056
  Dihedral  : 20.168 110.767   2561
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.49 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.10 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.33), residues: 688
  helix:  2.05 (0.25), residues: 466
  sheet: -0.71 (0.94), residues: 27
  loop : -0.32 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 753 
 TYR   0.019   0.001   TYR D 685 
 PHE   0.018   0.001   PHE C 144 
 TRP   0.007   0.002   TRP D 692 
 HIS   0.002   0.000   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8112)
  covalent geometry    : angle       0.54618 (11511)
  hydrogen bonds       : bond        0.03751 (  467)
  hydrogen bonds       : angle       3.77192 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  709 LEU cc_start: 0.8836 (tt) cc_final: 0.8344 (tp)
REVERT: A  713 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8038 (tm-30)
REVERT: A  716 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8300 (ttpt)
REVERT: D   42 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7184 (m-80)
REVERT: D  132 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7934 (mp10)
REVERT: D  146 ASP cc_start: 0.8307 (t0) cc_final: 0.8081 (t0)
REVERT: D  618 CYS cc_start: 0.9088 (t) cc_final: 0.8724 (t)
REVERT: C   80 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.6626 (t80)
REVERT: C  109 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7970 (pp)
  outliers start: 20
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1047
  time to fit residues: 13.6974
Evaluate side-chains
  95 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  712 LEU
Chi-restraints excluded: chain D residue  739 GLU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  130 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0980
   chunk 18 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 729 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.147588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.103294 restraints weight = 18130.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.27
r_work: 0.3438 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8112  Z= 0.139
  Angle     :  0.577   9.441  11511  Z= 0.287
  Chirality :  0.033   0.136   1433
  Planarity :  0.004   0.069   1056
  Dihedral  : 20.181 112.945   2561
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.49 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.05 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.33), residues: 688
  helix:  2.02 (0.25), residues: 466
  sheet: -0.80 (0.93), residues: 27
  loop : -0.34 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 753 
 TYR   0.020   0.001   TYR D 685 
 PHE   0.023   0.002   PHE C 104 
 TRP   0.005   0.002   TRP D 692 
 HIS   0.001   0.001   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8112)
  covalent geometry    : angle       0.57659 (11511)
  hydrogen bonds       : bond        0.03954 (  467)
  hydrogen bonds       : angle       3.80428 ( 1255)

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

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

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: A  716 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8410 (ttpt)
REVERT: B  709 LEU cc_start: 0.9239 (tt) cc_final: 0.8991 (mm)
REVERT: D   42 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7093 (m-80)
REVERT: D  132 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7978 (mp10)
REVERT: D  146 ASP cc_start: 0.8361 (t0) cc_final: 0.8147 (t0)
REVERT: D  608 HIS cc_start: 0.7343 (t-170) cc_final: 0.6991 (t70)
REVERT: D  618 CYS cc_start: 0.9094 (t) cc_final: 0.8742 (t)
REVERT: C   80 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.6633 (t80)
REVERT: C  105 LYS cc_start: 0.7856 (tptt) cc_final: 0.7552 (tptt)
  outliers start: 16
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0968
  time to fit residues: 12.0895
Evaluate side-chains
  91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue   42 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  712 LEU
Chi-restraints excluded: chain D residue  739 GLU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  130 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 15 optimal weight:    0.2980
   chunk 45 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0770
   chunk 16 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    0.5338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.147797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.105020 restraints weight = 17689.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.17
r_work: 0.3450 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8112  Z= 0.134
  Angle     :  0.584   8.982  11511  Z= 0.291
  Chirality :  0.032   0.135   1433
  Planarity :  0.004   0.075   1056
  Dihedral  : 20.185 112.844   2561
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.49 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.62 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.33), residues: 688
  helix:  1.98 (0.25), residues: 466
  sheet: -0.83 (0.94), residues: 27
  loop : -0.40 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 753 
 TYR   0.022   0.002   TYR D 685 
 PHE   0.013   0.002   PHE C 144 
 TRP   0.028   0.006   TRP D 692 
 HIS   0.001   0.000   HIS D 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8112)
  covalent geometry    : angle       0.58390 (11511)
  hydrogen bonds       : bond        0.03862 (  467)
  hydrogen bonds       : angle       3.78084 ( 1255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1978.55 seconds
wall clock time: 34 minutes 40.11 seconds (2080.11 seconds total)