Starting phenix.real_space_refine
on Wed Aug  5 01:06:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw6_54300/08_2026/9rw6_54300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw6_54300/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw6_54300/08_2026/9rw6_54300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw6_54300/08_2026/9rw6_54300.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw6_54300/08_2026/9rw6_54300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw6_54300/08_2026/9rw6_54300.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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-2.2rc3-6140/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: 1.92, 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: 0.74
  Conformation dependent library (CDL) restraints added in 350.0 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: 1.06
  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: 1.40

  Time building geometry restraints manager: 0.98 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: 11432
        2.99 -     5.97: 71
        5.97 -     8.96: 7
        8.96 -    11.95: 0
       11.95 -    14.94: 1
  Bond angle restraints: 11511
  Sorted by residual:
  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=" 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 2.20e+00 2.07e-01 4.61e+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=" O   ARG C  10 "
        pdb=" C   ARG C  10 "
        pdb=" N   ASN C  11 "
      ideal   model   delta    sigma   weight residual
     122.12  117.06    5.06 1.06e+00 8.90e-01 2.28e+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: 1142
       0.043 -    0.085: 134
       0.085 -    0.128: 152
       0.128 -    0.171: 3
       0.171 -    0.214: 2
  Chirality restraints: 1433
  Sorted by residual:
  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
  chirality pdb=" CA  LEU B 733 "
            pdb=" N   LEU B 733 "
            pdb=" C   LEU B 733 "
            pdb=" CB  LEU B 733 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.20e-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:             4.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.870
  Find NCS groups from input model:        0.050
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.220
-------------------------------------------------------------------------------
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= 0.341
  Angle     :  0.683  14.937  11511  Z= 0.515
  Chirality :  0.042   0.214   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        0.00469 /  0.34 ( 8112)
  covalent geometry    : angle       0.68310 /  0.51 (11511)
  hydrogen bonds       : bond        0.21332 / 14.71 (  467)
  hydrogen bonds       : angle       6.70570 /  6.15 ( 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  : 0.251 
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: 0.7687 (m-80)
REVERT: C  144 PHE cc_start: 0.7799 (t80) cc_final: 0.7327 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 110
  average time/residue: 0.1061
  time to fit residues: 15.1668
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  : 0.244 
-------------------------------------------------------------------------------
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:    6.9990
   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 = 0.146138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.102161 restraints weight = 18190.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.22
r_work: 0.3436 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8112  Z= 0.186
  Angle     :  0.645  11.472  11511  Z= 0.347
  Chirality :  0.041   0.288   1433
  Planarity :  0.004   0.044   1056
  Dihedral  : 20.612 142.348   2563
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  3.63 %
    Favored  : 95.93 %
  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:  1.12 (0.32), residues: 688
  helix:  1.51 (0.24), residues: 449
  sheet: -0.93 (0.82), residues: 33
  loop : -0.60 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 736 
 TYR   0.019   0.002   TYR D 685 
 PHE   0.013   0.002   PHE D 733 
 TRP   0.004   0.002   TRP D 692 
 HIS   0.008   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.19 ( 8112)
  covalent geometry    : angle       0.64507 /  0.35 (11511)
  hydrogen bonds       : bond        0.06513 /  4.55 (  467)
  hydrogen bonds       : angle       5.11503 /  4.68 ( 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
  105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8437 (ttpt)
REVERT: D  588 PHE cc_start: 0.7620 (t80) cc_final: 0.7284 (t80)
REVERT: D  710 LEU cc_start: 0.8708 (mm) cc_final: 0.8390 (mm)
REVERT: D  742 LEU cc_start: 0.8845 (mm) cc_final: 0.8376 (tp)
REVERT: C  144 PHE cc_start: 0.7789 (t80) cc_final: 0.7157 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1190
  time to fit residues: 15.1548
Evaluate side-chains
  87 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  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 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:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 73 optimal weight:   30.0000
   chunk 57 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4409 r_free = 0.4409 target = 0.147252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.106101 restraints weight = 18238.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.19
r_work: 0.3459 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8112  Z= 0.140
  Angle     :  0.566   9.839  11511  Z= 0.302
  Chirality :  0.037   0.251   1433
  Planarity :  0.004   0.048   1056
  Dihedral  : 20.548 135.666   2561
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.78 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.63 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.32), residues: 688
  helix:  1.56 (0.24), residues: 456
  sheet: -1.04 (0.78), residues: 33
  loop : -0.39 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG C 120 
 TYR   0.023   0.001   TYR D 685 
 PHE   0.019   0.002   PHE D 718 
 TRP   0.006   0.003   TRP D 692 
 HIS   0.004   0.001   HIS D 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.14 ( 8112)
  covalent geometry    : angle       0.56552 /  0.30 (11511)
  hydrogen bonds       : bond        0.05472 /  3.82 (  467)
  hydrogen bonds       : angle       4.71522 /  4.32 ( 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
  102 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8283 (ttpt)
REVERT: B  742 MET cc_start: 0.8916 (tmm) cc_final: 0.8695 (tmm)
REVERT: D  702 MET cc_start: 0.6782 (mmm) cc_final: 0.6538 (mpp)
REVERT: D  740 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7884 (tt0)
REVERT: C  144 PHE cc_start: 0.7768 (t80) cc_final: 0.7234 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 97
  average time/residue: 0.1163
  time to fit residues: 14.5438
Evaluate side-chains
  88 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue  122 LEU
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 D residue  792 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  123 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:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 68 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8786

-------------------------------------------------------------------------------
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 = 0.4396 r_free = 0.4396 target = 0.146439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.101560 restraints weight = 18386.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.32
r_work: 0.3432 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   8112  Z= 0.161
  Angle     :  0.579   9.510  11511  Z= 0.303
  Chirality :  0.038   0.241   1433
  Planarity :  0.005   0.102   1056
  Dihedral  : 20.505 133.932   2561
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.07 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 19.01 %
    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:  1.23 (0.32), residues: 688
  helix:  1.56 (0.24), residues: 457
  sheet: -1.26 (0.74), residues: 33
  loop : -0.45 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 757 
 TYR   0.020   0.001   TYR D 685 
 PHE   0.020   0.002   PHE D 718 
 TRP   0.013   0.003   TRP D 692 
 HIS   0.002   0.001   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 8112)
  covalent geometry    : angle       0.57859 /  0.30 (11511)
  hydrogen bonds       : bond        0.05254 /  3.65 (  467)
  hydrogen bonds       : angle       4.60380 /  4.25 ( 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
  114 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8243 (ttpt)
REVERT: B  742 MET cc_start: 0.8913 (tmm) cc_final: 0.8690 (tmm)
REVERT: D  146 ASP cc_start: 0.8402 (t0) cc_final: 0.8190 (t0)
REVERT: D  588 PHE cc_start: 0.7665 (t80) cc_final: 0.7104 (t80)
REVERT: D  685 TYR cc_start: 0.8240 (t80) cc_final: 0.7850 (t80)
REVERT: D  692 TRP cc_start: 0.7246 (m100) cc_final: 0.6959 (m100)
REVERT: D  742 LEU cc_start: 0.8811 (mm) cc_final: 0.8372 (tp)
REVERT: C  144 PHE cc_start: 0.7693 (t80) cc_final: 0.7266 (t80)
  outliers start: 28
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0962
  time to fit residues: 14.0910
Evaluate side-chains
  90 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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  122 LEU
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  586 PHE
Chi-restraints excluded: chain D residue  739 GLU
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  792 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  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:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:   20.0000
   chunk 43 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4397 r_free = 0.4397 target = 0.146479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.100607 restraints weight = 18299.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.02
r_work: 0.3474 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2339

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= 0.158
  Angle     :  0.586   8.598  11511  Z= 0.305
  Chirality :  0.037   0.218   1433
  Planarity :  0.004   0.061   1056
  Dihedral  : 20.478 131.664   2561
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.36 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 19.77 %
    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:  1.27 (0.32), residues: 688
  helix:  1.60 (0.24), residues: 458
  sheet: -1.46 (0.73), residues: 33
  loop : -0.42 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.024   0.002   TYR D 549 
 PHE   0.022   0.002   PHE D 718 
 TRP   0.009   0.002   TRP D 692 
 HIS   0.002   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 8112)
  covalent geometry    : angle       0.58558 /  0.30 (11511)
  hydrogen bonds       : bond        0.05037 /  3.50 (  467)
  hydrogen bonds       : angle       4.49023 /  4.13 ( 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: 24
    poor density    : 85
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  716 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8192 (ttpt)
REVERT: B  742 MET cc_start: 0.8879 (tmm) cc_final: 0.8644 (tmm)
REVERT: D  126 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8106 (ttt90)
REVERT: D  146 ASP cc_start: 0.8384 (t0) cc_final: 0.8167 (t0)
REVERT: D  588 PHE cc_start: 0.7743 (t80) cc_final: 0.7323 (t80)
REVERT: D  685 TYR cc_start: 0.8084 (t80) cc_final: 0.7786 (t80)
REVERT: D  692 TRP cc_start: 0.7241 (m100) cc_final: 0.6974 (m100)
REVERT: D  790 MET cc_start: 0.8047 (tmm) cc_final: 0.7405 (tmm)
REVERT: C  123 LEU cc_start: 0.8065 (mt) cc_final: 0.7829 (mt)
REVERT: C  144 PHE cc_start: 0.7638 (t80) cc_final: 0.7279 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 102
  average time/residue: 0.0996
  time to fit residues: 13.4048
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  : 0.238 
-------------------------------------------------------------------------------
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   76 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  126 ARG
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  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  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:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   chunk 71 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.147164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.112813 restraints weight = 18409.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 4.02
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8112  Z= 0.136
  Angle     :  0.562   7.712  11511  Z= 0.292
  Chirality :  0.036   0.190   1433
  Planarity :  0.004   0.046   1056
  Dihedral  : 20.431 129.178   2561
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.78 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.10 %
    Favored  : 75.29 %
  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:  1.72 (0.24), residues: 458
  sheet: -1.51 (0.73), residues: 33
  loop : -0.38 (0.47), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  10 
 TYR   0.015   0.001   TYR D 685 
 PHE   0.023   0.002   PHE D 718 
 TRP   0.009   0.002   TRP D 692 
 HIS   0.002   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.14 ( 8112)
  covalent geometry    : angle       0.56159 /  0.29 (11511)
  hydrogen bonds       : bond        0.04728 /  3.28 (  467)
  hydrogen bonds       : angle       4.32387 /  3.97 ( 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: 19
    poor density    : 82
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7933 (ttpt)
REVERT: B  742 MET cc_start: 0.8555 (tmm) cc_final: 0.8345 (tmm)
REVERT: D  126 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7854 (ttt90)
REVERT: D  146 ASP cc_start: 0.7777 (t0) cc_final: 0.7540 (t0)
REVERT: D  742 LEU cc_start: 0.7959 (mm) cc_final: 0.7649 (tp)
REVERT: D  790 MET cc_start: 0.7715 (tmm) cc_final: 0.7211 (tmm)
  outliers start: 19
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1129
  time to fit residues: 14.1910
Evaluate side-chains
  93 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LYS
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  126 ARG
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  739 GLU
Chi-restraints excluded: chain D residue  784 ILE
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   97 ILE
Chi-restraints excluded: chain C residue  109 LEU
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:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 36 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.4404 r_free = 0.4404 target = 0.146900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.112709 restraints weight = 18366.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 3.88
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8112  Z= 0.150
  Angle     :  0.580   7.754  11511  Z= 0.303
  Chirality :  0.036   0.164   1433
  Planarity :  0.005   0.101   1056
  Dihedral  : 20.404 127.463   2561
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.10 %
    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:  1.46 (0.33), residues: 688
  helix:  1.71 (0.24), residues: 458
  sheet: -1.21 (0.81), residues: 33
  loop : -0.33 (0.47), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 126 
 TYR   0.028   0.002   TYR D 685 
 PHE   0.031   0.003   PHE D 588 
 TRP   0.014   0.004   TRP D 692 
 HIS   0.002   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 8112)
  covalent geometry    : angle       0.58049 /  0.30 (11511)
  hydrogen bonds       : bond        0.04795 /  3.35 (  467)
  hydrogen bonds       : angle       4.30796 /  3.98 ( 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
  103 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7945 (ttpt)
REVERT: B  742 MET cc_start: 0.8530 (tmm) cc_final: 0.8326 (tmm)
REVERT: D  146 ASP cc_start: 0.7728 (t0) cc_final: 0.7499 (t0)
REVERT: D  790 MET cc_start: 0.7629 (tmm) cc_final: 0.7112 (tmm)
  outliers start: 21
  outliers final: 15
  residues processed: 97
  average time/residue: 0.1032
  time to fit residues: 13.2859
Evaluate side-chains
  93 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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   76 GLN
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  739 GLU
Chi-restraints excluded: chain D residue  784 ILE
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  157 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 77 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 73 optimal weight:   30.0000
   chunk 30 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 66 optimal weight:    0.2980
   chunk 68 optimal weight:    0.5980
   chunk 37 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0870
   overall best weight:    0.3476

-------------------------------------------------------------------------------
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 = 0.4416 r_free = 0.4416 target = 0.147722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.113310 restraints weight = 18378.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 3.98
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8112  Z= 0.122
  Angle     :  0.574   8.547  11511  Z= 0.295
  Chirality :  0.035   0.217   1433
  Planarity :  0.005   0.098   1056
  Dihedral  : 20.354 124.568   2561
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.49 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.24 %
    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:  1.49 (0.33), residues: 688
  helix:  1.77 (0.24), residues: 464
  sheet: -1.08 (0.84), residues: 33
  loop : -0.52 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 120 
 TYR   0.024   0.001   TYR D 685 
 PHE   0.041   0.002   PHE C 144 
 TRP   0.004   0.001   TRP D 692 
 HIS   0.002   0.000   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 ( 8112)
  covalent geometry    : angle       0.57439 /  0.30 (11511)
  hydrogen bonds       : bond        0.04430 /  3.10 (  467)
  hydrogen bonds       : angle       4.15341 /  3.80 ( 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
  96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7974 (ttpt)
REVERT: B  733 LEU cc_start: 0.8771 (tp) cc_final: 0.8538 (tt)
REVERT: D  146 ASP cc_start: 0.7663 (t0) cc_final: 0.7396 (t0)
REVERT: D  742 LEU cc_start: 0.8112 (mp) cc_final: 0.7783 (tp)
REVERT: D  790 MET cc_start: 0.7551 (tmm) cc_final: 0.7055 (tmm)
  outliers start: 15
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0973
  time to fit residues: 11.9002
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  : 0.268 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  126 ARG
Chi-restraints excluded: chain D residue  739 GLU
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  109 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  130 SER
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:    0.0980
   chunk 20 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 41 optimal weight:    0.2980
   chunk 66 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4414 r_free = 0.4414 target = 0.147572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.113776 restraints weight = 18272.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 4.05
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2914

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= 0.128
  Angle     :  0.559   8.127  11511  Z= 0.291
  Chirality :  0.034   0.151   1433
  Planarity :  0.005   0.093   1056
  Dihedral  : 20.297 121.047   2561
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.92 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.05 %
    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:  1.54 (0.33), residues: 688
  helix:  1.81 (0.24), residues: 464
  sheet: -1.05 (0.86), residues: 33
  loop : -0.49 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 753 
 TYR   0.027   0.001   TYR D 685 
 PHE   0.033   0.002   PHE D 718 
 TRP   0.005   0.002   TRP D 692 
 HIS   0.002   0.000   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 8112)
  covalent geometry    : angle       0.55862 /  0.29 (11511)
  hydrogen bonds       : bond        0.04432 /  3.09 (  467)
  hydrogen bonds       : angle       4.08620 /  3.74 ( 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
  96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7961 (ttpt)
REVERT: B  733 LEU cc_start: 0.8768 (tp) cc_final: 0.8549 (tt)
REVERT: D  146 ASP cc_start: 0.7642 (t0) cc_final: 0.7381 (t0)
REVERT: D  742 LEU cc_start: 0.8188 (mp) cc_final: 0.7857 (tp)
  outliers start: 18
  outliers final: 15
  residues processed: 90
  average time/residue: 0.0937
  time to fit residues: 11.3354
Evaluate side-chains
  92 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  126 ARG
Chi-restraints excluded: chain D residue  586 PHE
Chi-restraints excluded: chain D residue  739 GLU
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  130 SER
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:    0.3980
   chunk 22 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 73 optimal weight:   20.0000
   chunk 64 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4415 r_free = 0.4415 target = 0.147738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.114249 restraints weight = 18418.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 4.22
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.3026

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= 0.135
  Angle     :  0.581   8.577  11511  Z= 0.301
  Chirality :  0.035   0.218   1433
  Planarity :  0.004   0.083   1056
  Dihedral  : 20.257 117.419   2561
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.78 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.05 %
    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:  1.53 (0.33), residues: 688
  helix:  1.79 (0.25), residues: 464
  sheet: -1.15 (0.86), residues: 33
  loop : -0.46 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 120 
 TYR   0.054   0.002   TYR D 685 
 PHE   0.023   0.002   PHE D 588 
 TRP   0.036   0.009   TRP D 692 
 HIS   0.002   0.000   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 8112)
  covalent geometry    : angle       0.58128 /  0.30 (11511)
  hydrogen bonds       : bond        0.04405 /  3.07 (  467)
  hydrogen bonds       : angle       4.03452 /  3.70 ( 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: 18
    poor density    : 79
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: A  716 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8007 (ttpt)
REVERT: B  733 LEU cc_start: 0.8786 (tp) cc_final: 0.8555 (tt)
REVERT: D  146 ASP cc_start: 0.7718 (t0) cc_final: 0.7466 (t0)
REVERT: D  742 LEU cc_start: 0.8212 (mp) cc_final: 0.7898 (tp)
REVERT: D  790 MET cc_start: 0.7745 (tmm) cc_final: 0.7294 (tmm)
  outliers start: 18
  outliers final: 13
  residues processed: 90
  average time/residue: 0.0939
  time to fit residues: 11.4559
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  : 0.229 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  586 PHE
Chi-restraints excluded: chain D residue  739 GLU
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  130 SER
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 45 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 8 optimal weight:   20.0000
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.4415 r_free = 0.4415 target = 0.147645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.102625 restraints weight = 18256.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.43
r_work: 0.3462 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3094

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= 0.132
  Angle     :  0.584  10.961  11511  Z= 0.301
  Chirality :  0.034   0.170   1433
  Planarity :  0.004   0.077   1056
  Dihedral  : 20.220 114.908   2561
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.92 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.24 %
    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:  1.58 (0.33), residues: 688
  helix:  1.82 (0.25), residues: 465
  sheet: -0.94 (0.88), residues: 32
  loop : -0.46 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 753 
 TYR   0.024   0.001   TYR D 685 
 PHE   0.021   0.002   PHE C 144 
 TRP   0.022   0.005   TRP D 692 
 HIS   0.002   0.000   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 8112)
  covalent geometry    : angle       0.58375 /  0.30 (11511)
  hydrogen bonds       : bond        0.04374 /  3.04 (  467)
  hydrogen bonds       : angle       3.98654 /  3.66 ( 1255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1890.66 seconds
wall clock time: 33 minutes 13.75 seconds (1993.75 seconds total)