Starting phenix.real_space_refine
on Thu Jul  2 08:42:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw6_54300/07_2026/9rw6_54300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw6_54300/07_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_54300/07_2026/9rw6_54300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw6_54300/07_2026/9rw6_54300.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw6_54300/07_2026/9rw6_54300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw6_54300/07_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 1.43, per 1000 atoms: 0.18
  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: 0.63
  Conformation dependent library (CDL) restraints added in 283.0 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: 0.76
  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: 1.29

  Time building geometry restraints manager: 0.82 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:             3.110
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.620
  Find NCS groups from input model:        0.030
  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:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
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= 0.331
  Angle     :  0.592  14.937  11511  Z= 0.426
  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/Z
  covalent geometry    : bond        0.00461 /  0.33 ( 8112)
  covalent geometry    : angle       0.59163 /  0.43 (11511)
  hydrogen bonds       : bond        0.21332 / 14.71 (  467)
  hydrogen bonds       : angle       6.70570 /  6.06 ( 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  : 0.181 
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: 0.0894
  time to fit residues: 12.7121
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  : 0.198 
-------------------------------------------------------------------------------
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:    4.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 538 GLN
D 624 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.146215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.111484 restraints weight = 18219.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 4.09
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8112  Z= 0.185
  Angle     :  0.622   8.651  11511  Z= 0.343
  Chirality :  0.039   0.178   1433
  Planarity :  0.004   0.044   1056
  Dihedral  : 20.714 145.666   2563
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.01 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.07 (0.32), residues: 688
  helix:  1.46 (0.24), residues: 449
  sheet: -0.91 (0.82), residues: 33
  loop : -0.61 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 736 
 TYR   0.021   0.002   TYR D 704 
 PHE   0.013   0.002   PHE D 733 
 TRP   0.007   0.003   TRP D 692 
 HIS   0.009   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 ( 8112)
  covalent geometry    : angle       0.62215 /  0.34 (11511)
  hydrogen bonds       : bond        0.06346 /  4.45 (  467)
  hydrogen bonds       : angle       5.10859 /  4.59 ( 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
  104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8136 (ttpt)
REVERT: D  560 LEU cc_start: 0.7851 (mp) cc_final: 0.7632 (mt)
REVERT: D  588 PHE cc_start: 0.6477 (t80) cc_final: 0.6193 (t80)
REVERT: D  710 LEU cc_start: 0.7867 (mm) cc_final: 0.7609 (mm)
REVERT: D  742 LEU cc_start: 0.8109 (mm) cc_final: 0.7687 (tp)
REVERT: C  144 PHE cc_start: 0.7526 (t80) cc_final: 0.7108 (t80)
  outliers start: 13
  outliers final: 7
  residues processed: 98
  average time/residue: 0.0998
  time to fit residues: 12.6083
Evaluate side-chains
  90 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  587 LEU
Chi-restraints excluded: chain D residue  712 LEU
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue   70 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:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 73 optimal weight:   20.0000
   chunk 57 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 106 ASN
D 740 GLN
C 151 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.146279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.111277 restraints weight = 18104.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 3.91
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8112  Z= 0.164
  Angle     :  0.552   7.694  11511  Z= 0.304
  Chirality :  0.035   0.171   1433
  Planarity :  0.004   0.042   1056
  Dihedral  : 20.671 138.218   2561
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.78 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.01 %
    Favored  : 77.76 %
  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:  1.24 (0.32), residues: 688
  helix:  1.53 (0.24), residues: 457
  sheet: -1.10 (0.79), residues: 33
  loop : -0.39 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 753 
 TYR   0.023   0.002   TYR D 685 
 PHE   0.014   0.002   PHE D  17 
 TRP   0.008   0.003   TRP D 692 
 HIS   0.004   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 ( 8112)
  covalent geometry    : angle       0.55197 /  0.30 (11511)
  hydrogen bonds       : bond        0.05584 /  3.88 (  467)
  hydrogen bonds       : angle       4.75770 /  4.30 ( 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
  100 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8031 (ttpt)
REVERT: D  740 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8145 (tt0)
REVERT: C  144 PHE cc_start: 0.7517 (t80) cc_final: 0.7253 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 97
  average time/residue: 0.0990
  time to fit residues: 12.3438
Evaluate side-chains
  86 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  740 GLN
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  109 LEU
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:    8.9990
   chunk 44 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0980
   chunk 11 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 62 optimal weight:    0.2980
   chunk 24 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 740 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.147235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.102598 restraints weight = 18404.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.39
r_work: 0.3451 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   8112  Z= 0.136
  Angle     :  0.545   7.798  11511  Z= 0.293
  Chirality :  0.035   0.192   1433
  Planarity :  0.005   0.098   1056
  Dihedral  : 20.614 135.800   2561
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.39 %
    Favored  : 75.86 %
  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:  1.33 (0.33), residues: 688
  helix:  1.61 (0.24), residues: 457
  sheet: -1.32 (0.76), residues: 33
  loop : -0.35 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  10 
 TYR   0.018   0.002   TYR D 549 
 PHE   0.012   0.002   PHE D 691 
 TRP   0.012   0.003   TRP D 692 
 HIS   0.003   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.14 ( 8112)
  covalent geometry    : angle       0.54470 /  0.29 (11511)
  hydrogen bonds       : bond        0.04952 /  3.46 (  467)
  hydrogen bonds       : angle       4.56343 /  4.14 ( 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
  113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  716 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8251 (ttpt)
REVERT: D  146 ASP cc_start: 0.8406 (t0) cc_final: 0.8200 (t0)
REVERT: D  588 PHE cc_start: 0.7732 (t80) cc_final: 0.7197 (t80)
REVERT: D  685 TYR cc_start: 0.8200 (t80) cc_final: 0.7801 (t80)
REVERT: D  692 TRP cc_start: 0.7222 (m100) cc_final: 0.6983 (m100)
REVERT: D  742 LEU cc_start: 0.8801 (mm) cc_final: 0.8332 (tp)
REVERT: D  790 MET cc_start: 0.8070 (tmm) cc_final: 0.7600 (tmm)
REVERT: C  144 PHE cc_start: 0.7669 (t80) cc_final: 0.7153 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0991
  time to fit residues: 14.1501
Evaluate side-chains
  92 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain D residue  132 GLN
Chi-restraints excluded: chain D residue  586 PHE
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  786 LEU
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  133 VAL
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:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 43 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0270
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5642

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.147024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.112303 restraints weight = 18264.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 3.92
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8112  Z= 0.139
  Angle     :  0.559   9.032  11511  Z= 0.296
  Chirality :  0.035   0.180   1433
  Planarity :  0.005   0.091   1056
  Dihedral  : 20.559 132.953   2561
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.07 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 20.34 %
    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:  1.32 (0.33), residues: 688
  helix:  1.65 (0.24), residues: 456
  sheet: -1.51 (0.74), residues: 33
  loop : -0.44 (0.46), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 757 
 TYR   0.017   0.001   TYR D 685 
 PHE   0.021   0.002   PHE D 718 
 TRP   0.010   0.002   TRP D 692 
 HIS   0.002   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 ( 8112)
  covalent geometry    : angle       0.55910 /  0.30 (11511)
  hydrogen bonds       : bond        0.04801 /  3.34 (  467)
  hydrogen bonds       : angle       4.44446 /  4.01 ( 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
  109 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  716 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7900 (ttpt)
REVERT: D  146 ASP cc_start: 0.7716 (t0) cc_final: 0.7499 (t0)
REVERT: D  588 PHE cc_start: 0.6293 (t80) cc_final: 0.6042 (t80)
REVERT: D  790 MET cc_start: 0.7740 (tmm) cc_final: 0.7472 (tmm)
  outliers start: 22
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0980
  time to fit residues: 13.4813
Evaluate side-chains
  92 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue  117 VAL
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  586 PHE
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  141 ILE
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:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0670
   chunk 20 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6118

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.147107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.112018 restraints weight = 18208.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 3.99
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8112  Z= 0.140
  Angle     :  0.573   8.262  11511  Z= 0.301
  Chirality :  0.034   0.168   1433
  Planarity :  0.004   0.042   1056
  Dihedral  : 20.500 130.740   2561
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 21.10 %
    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:  1.38 (0.33), residues: 688
  helix:  1.70 (0.24), residues: 457
  sheet: -1.52 (0.73), residues: 33
  loop : -0.41 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 757 
 TYR   0.019   0.002   TYR D 685 
 PHE   0.016   0.002   PHE D 718 
 TRP   0.020   0.005   TRP D 692 
 HIS   0.002   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 ( 8112)
  covalent geometry    : angle       0.57344 /  0.30 (11511)
  hydrogen bonds       : bond        0.04737 /  3.30 (  467)
  hydrogen bonds       : angle       4.33999 /  3.93 ( 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
  101 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  716 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7924 (ttpt)
REVERT: D  146 ASP cc_start: 0.7781 (t0) cc_final: 0.7553 (t0)
REVERT: D  790 MET cc_start: 0.7741 (tmm) cc_final: 0.7491 (tmm)
  outliers start: 18
  outliers final: 13
  residues processed: 98
  average time/residue: 0.1053
  time to fit residues: 13.4300
Evaluate side-chains
  96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  586 PHE
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  786 LEU
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   97 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.0986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.145920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.110399 restraints weight = 18270.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 3.89
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8112  Z= 0.185
  Angle     :  0.598   9.188  11511  Z= 0.314
  Chirality :  0.036   0.182   1433
  Planarity :  0.005   0.124   1056
  Dihedral  : 20.463 128.472   2561
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.07 %
    Favored  : 95.64 %
  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:  1.41 (0.33), residues: 688
  helix:  1.68 (0.24), residues: 459
  sheet: -1.23 (0.83), residues: 33
  loop : -0.36 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 126 
 TYR   0.023   0.002   TYR D 685 
 PHE   0.023   0.002   PHE C 104 
 TRP   0.007   0.002   TRP D 692 
 HIS   0.003   0.001   HIS D  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.19 ( 8112)
  covalent geometry    : angle       0.59841 /  0.31 (11511)
  hydrogen bonds       : bond        0.05015 /  3.47 (  467)
  hydrogen bonds       : angle       4.36877 /  3.99 ( 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
  99 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  716 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7900 (ttpt)
REVERT: B  733 LEU cc_start: 0.8781 (tp) cc_final: 0.8574 (tt)
REVERT: D  146 ASP cc_start: 0.7692 (t0) cc_final: 0.7473 (t0)
REVERT: D  790 MET cc_start: 0.7725 (tmm) cc_final: 0.7497 (tmm)
  outliers start: 19
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0860
  time to fit residues: 10.9068
Evaluate side-chains
  91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
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 D residue  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  784 ILE
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   97 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  145 THR
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 73 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.144950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.109660 restraints weight = 18164.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 3.97
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8112  Z= 0.226
  Angle     :  0.633   8.680  11511  Z= 0.333
  Chirality :  0.038   0.176   1433
  Planarity :  0.006   0.116   1056
  Dihedral  : 20.498 124.712   2561
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.65 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.48 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.24 (0.33), residues: 688
  helix:  1.60 (0.24), residues: 452
  sheet: -1.26 (0.84), residues: 33
  loop : -0.51 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 120 
 TYR   0.023   0.002   TYR D 685 
 PHE   0.028   0.003   PHE D 718 
 TRP   0.004   0.002   TRP D 692 
 HIS   0.014   0.002   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00499 /  0.23 ( 8112)
  covalent geometry    : angle       0.63253 /  0.33 (11511)
  hydrogen bonds       : bond        0.05411 /  3.73 (  467)
  hydrogen bonds       : angle       4.41255 /  4.05 ( 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
  97 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  713 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8075 (tm-30)
REVERT: A  716 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8024 (ttpt)
REVERT: B  709 LEU cc_start: 0.9068 (tt) cc_final: 0.8811 (tt)
REVERT: B  733 LEU cc_start: 0.8812 (tp) cc_final: 0.8592 (tt)
REVERT: B  736 ARG cc_start: 0.8523 (tmm-80) cc_final: 0.8312 (tmm-80)
REVERT: D  146 ASP cc_start: 0.7801 (t0) cc_final: 0.7589 (t0)
REVERT: D  742 LEU cc_start: 0.8016 (mm) cc_final: 0.7741 (tp)
REVERT: D  790 MET cc_start: 0.7864 (tmm) cc_final: 0.7584 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 90
  average time/residue: 0.0931
  time to fit residues: 11.3921
Evaluate side-chains
  91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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 D residue  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  679 ASP
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain D residue  792 LEU
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   97 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0970
   chunk 60 optimal weight:    0.2980
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.5178

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.146782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.112058 restraints weight = 18170.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 4.05
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8112  Z= 0.137
  Angle     :  0.580   8.441  11511  Z= 0.304
  Chirality :  0.034   0.159   1433
  Planarity :  0.005   0.102   1056
  Dihedral  : 20.461 120.151   2561
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.78 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 23.57 %
    Favored  : 73.57 %
  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:  1.30 (0.33), residues: 688
  helix:  1.65 (0.24), residues: 465
  sheet: -1.16 (0.86), residues: 33
  loop : -0.65 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 120 
 TYR   0.045   0.002   TYR D 685 
 PHE   0.022   0.002   PHE C 104 
 TRP   0.024   0.006   TRP D 692 
 HIS   0.003   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 8112)
  covalent geometry    : angle       0.58023 /  0.30 (11511)
  hydrogen bonds       : bond        0.04574 /  3.18 (  467)
  hydrogen bonds       : angle       4.19751 /  3.81 ( 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
  93 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8030 (tm-30)
REVERT: A  716 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7916 (ttpt)
REVERT: B  709 LEU cc_start: 0.8992 (tt) cc_final: 0.8732 (tt)
REVERT: B  733 LEU cc_start: 0.8760 (tp) cc_final: 0.8548 (tt)
REVERT: D  146 ASP cc_start: 0.7668 (t0) cc_final: 0.7422 (t0)
REVERT: D  742 LEU cc_start: 0.7883 (mm) cc_final: 0.7653 (tp)
  outliers start: 15
  outliers final: 10
  residues processed: 89
  average time/residue: 0.0882
  time to fit residues: 10.5801
Evaluate side-chains
  88 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  586 PHE
Chi-restraints excluded: chain D residue  784 ILE
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  141 ILE
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 59 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 73 optimal weight:   20.0000
   chunk 64 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.5980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.146499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.100604 restraints weight = 18024.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.02
r_work: 0.3464 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8112  Z= 0.142
  Angle     :  0.582   9.056  11511  Z= 0.304
  Chirality :  0.034   0.198   1433
  Planarity :  0.005   0.092   1056
  Dihedral  : 20.407 117.762   2561
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.22 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 24.14 %
    Favored  : 73.57 %
  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:  1.31 (0.33), residues: 688
  helix:  1.63 (0.24), residues: 466
  sheet: -1.18 (0.87), residues: 33
  loop : -0.58 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 120 
 TYR   0.037   0.002   TYR D 685 
 PHE   0.024   0.002   PHE D 588 
 TRP   0.015   0.003   TRP D 692 
 HIS   0.002   0.001   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 8112)
  covalent geometry    : angle       0.58228 /  0.30 (11511)
  hydrogen bonds       : bond        0.04566 /  3.18 (  467)
  hydrogen bonds       : angle       4.15983 /  3.78 ( 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
  91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: A  716 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8297 (ttpt)
REVERT: B  709 LEU cc_start: 0.9155 (tt) cc_final: 0.8923 (tt)
REVERT: D  146 ASP cc_start: 0.8338 (t0) cc_final: 0.8068 (t0)
REVERT: D  742 LEU cc_start: 0.8852 (mm) cc_final: 0.8312 (tp)
  outliers start: 12
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1084
  time to fit residues: 12.5679
Evaluate side-chains
  88 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  586 PHE
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  141 ILE
Chi-restraints excluded: chain C residue  157 VAL
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:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:    0.5980
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.146509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.101090 restraints weight = 18179.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.48
r_work: 0.3436 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8112  Z= 0.148
  Angle     :  0.592   8.535  11511  Z= 0.305
  Chirality :  0.034   0.168   1433
  Planarity :  0.004   0.086   1056
  Dihedral  : 20.374 116.372   2561
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.07 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 24.71 %
    Favored  : 73.19 %
  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:  1.28 (0.33), residues: 688
  helix:  1.60 (0.24), residues: 466
  sheet: -1.14 (0.88), residues: 33
  loop : -0.59 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 120 
 TYR   0.025   0.002   TYR D 685 
 PHE   0.018   0.002   PHE C 104 
 TRP   0.016   0.003   TRP D 692 
 HIS   0.002   0.001   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.15 ( 8112)
  covalent geometry    : angle       0.59175 /  0.30 (11511)
  hydrogen bonds       : bond        0.04570 /  3.18 (  467)
  hydrogen bonds       : angle       4.13614 /  3.77 ( 1255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1641.03 seconds
wall clock time: 29 minutes 3.41 seconds (1743.41 seconds total)