Starting phenix.real_space_refine
on Fri Sep 11 21:21:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x3x_32996/09_2026/7x3x_32996.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x3x_32996/09_2026/7x3x_32996.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x3x_32996/09_2026/7x3x_32996.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x3x_32996/09_2026/7x3x_32996.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x3x_32996/09_2026/7x3x_32996.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x3x_32996/09_2026/7x3x_32996.cif"
  }
  resolution = 3.2
  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=   0.002
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     292      5.49       5
     S      12      5.16       5
     C    6647      2.51       5
     N    2257      2.21       5
     O    2828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12036
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 811
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "D"
      Number of atoms: 717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 717
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 672
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "G"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 815
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "H"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2978
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3008
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "V"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 62
          Classifications: {'peptide': 7}
          Link IDs: {'PTRANS': 1, 'TRANS': 5}
  Time building chain proxies: 2.14, per 1000 atoms: 0.18
  Number of scatterers: 12036
  At special positions: 0
  Unit cell: (93.095, 125.57, 116.91, 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      12     16.00
     P     292     15.00
     O    2828      8.00
     N    2257      7.00
     C    6647      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: 0.89
  Conformation dependent library (CDL) restraints added in 345.1 milliseconds
  

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      70.9% alpha, 2.6% beta
      137 base pairs and 225 stacking pairs defined.
    Time for finding SS restraints: 1.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.754A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.969A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.810A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.485A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.686A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.802A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.422A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.603A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.706A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.886A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 7.123A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.991A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.547A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    406 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      351 hydrogen bonds
      702 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      225 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.12 -     1.27: 1258
        1.27 -     1.41: 3834
        1.41 -     1.55: 7099
        1.55 -     1.69: 624
        1.69 -     1.83: 28
  Bond restraints: 12843
  Sorted by residual:
  bond pdb=" C3'  DA I  90 "
       pdb=" O3'  DA I  90 "
    ideal  model  delta    sigma   weight residual
    1.435  1.823 -0.388 1.30e-02 5.92e+03 8.89e+02
  bond pdb=" C1'  DT I  87 "
       pdb=" N1   DT I  87 "
    ideal  model  delta    sigma   weight residual
    1.468  1.830 -0.362 1.40e-02 5.10e+03 6.68e+02
  bond pdb=" C1'  DT I  89 "
       pdb=" N1   DT I  89 "
    ideal  model  delta    sigma   weight residual
    1.468  1.125  0.343 1.40e-02 5.10e+03 6.01e+02
  bond pdb=" N7   DG J  55 "
       pdb=" C5   DG J  55 "
    ideal  model  delta    sigma   weight residual
    1.388  1.254  0.134 6.00e-03 2.78e+04 4.96e+02
  bond pdb=" N9   DG J  55 "
       pdb=" C8   DG J  55 "
    ideal  model  delta    sigma   weight residual
    1.374  1.239  0.135 7.00e-03 2.04e+04 3.71e+02
  ... (remaining 12838 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.17: 18453
        4.17 -     8.35: 113
        8.35 -    12.52: 32
       12.52 -    16.69: 7
       16.69 -    20.87: 5
  Bond angle restraints: 18610
  Sorted by residual:
  angle pdb=" O4'  DT I  88 "
        pdb=" C1'  DT I  88 "
        pdb=" N1   DT I  88 "
      ideal   model   delta    sigma   weight residual
     108.00  121.03  -13.03 7.00e-01 2.04e+00 3.46e+02
  angle pdb=" O5'  DG J  53 "
        pdb=" C5'  DG J  53 "
        pdb=" C4'  DG J  53 "
      ideal   model   delta    sigma   weight residual
     109.40  121.17  -11.77 8.00e-01 1.56e+00 2.16e+02
  angle pdb=" O5'  DA I  91 "
        pdb=" C5'  DA I  91 "
        pdb=" C4'  DA I  91 "
      ideal   model   delta    sigma   weight residual
     109.40  120.89  -11.49 8.00e-01 1.56e+00 2.06e+02
  angle pdb=" O4'  DA I  91 "
        pdb=" C4'  DA I  91 "
        pdb=" C3'  DA I  91 "
      ideal   model   delta    sigma   weight residual
     106.00   98.03    7.97 6.00e-01 2.78e+00 1.76e+02
  angle pdb=" O5'  DG J  56 "
        pdb=" C5'  DG J  56 "
        pdb=" C4'  DG J  56 "
      ideal   model   delta    sigma   weight residual
     109.40  119.68  -10.28 8.00e-01 1.56e+00 1.65e+02
  ... (remaining 18605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.19: 5604
       35.19 -    70.37: 1333
       70.37 -   105.56: 27
      105.56 -   140.74: 1
      140.74 -   175.92: 2
  Dihedral angle restraints: 6967
    sinusoidal: 4733
      harmonic: 2234
  Sorted by residual:
  dihedral pdb=" CA  LYS B  20 "
           pdb=" C   LYS B  20 "
           pdb=" N   VAL B  21 "
           pdb=" CA  VAL B  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.00   39.00     0      5.00e+00 4.00e-02 6.08e+01
  dihedral pdb=" CA  ARG B  19 "
           pdb=" C   ARG B  19 "
           pdb=" N   LYS B  20 "
           pdb=" CA  LYS B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.89  -26.11     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" C4'  DG J  94 "
           pdb=" C3'  DG J  94 "
           pdb=" O3'  DG J  94 "
           pdb=" P    DG J  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.08  175.92     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 6964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.156: 2083
       0.156 -    0.313: 31
       0.313 -    0.469: 7
       0.469 -    0.626: 3
       0.626 -    0.782: 3
  Chirality restraints: 2127
  Sorted by residual:
  chirality pdb=" P    DT I  89 "
            pdb=" OP1  DT I  89 "
            pdb=" OP2  DT I  89 "
            pdb=" O5'  DT I  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -1.55    0.78 2.00e-01 2.50e+01 1.53e+01
  chirality pdb=" C1'  DA I  90 "
            pdb=" O4'  DA I  90 "
            pdb=" C2'  DA I  90 "
            pdb=" N9   DA I  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.77    0.67 2.00e-01 2.50e+01 1.11e+01
  chirality pdb=" C1'  DT I  89 "
            pdb=" O4'  DT I  89 "
            pdb=" C2'  DT I  89 "
            pdb=" N1   DT I  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.79    0.64 2.00e-01 2.50e+01 1.04e+01
  ... (remaining 2124 not shown)

  Planarity restraints: 1347
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  55 "    0.071 2.00e-02 2.50e+03   6.85e-02 1.41e+02
        pdb=" N9   DG J  55 "   -0.203 2.00e-02 2.50e+03
        pdb=" C8   DG J  55 "    0.030 2.00e-02 2.50e+03
        pdb=" N7   DG J  55 "    0.065 2.00e-02 2.50e+03
        pdb=" C5   DG J  55 "    0.012 2.00e-02 2.50e+03
        pdb=" C6   DG J  55 "    0.035 2.00e-02 2.50e+03
        pdb=" O6   DG J  55 "   -0.053 2.00e-02 2.50e+03
        pdb=" N1   DG J  55 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2   DG J  55 "    0.008 2.00e-02 2.50e+03
        pdb=" N2   DG J  55 "    0.008 2.00e-02 2.50e+03
        pdb=" N3   DG J  55 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DG J  55 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  54 "    0.074 2.00e-02 2.50e+03   4.96e-02 5.54e+01
        pdb=" N1   DC J  54 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2   DC J  54 "   -0.062 2.00e-02 2.50e+03
        pdb=" O2   DC J  54 "    0.033 2.00e-02 2.50e+03
        pdb=" N3   DC J  54 "   -0.026 2.00e-02 2.50e+03
        pdb=" C4   DC J  54 "   -0.052 2.00e-02 2.50e+03
        pdb=" N4   DC J  54 "    0.081 2.00e-02 2.50e+03
        pdb=" C5   DC J  54 "    0.010 2.00e-02 2.50e+03
        pdb=" C6   DC J  54 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  89 "    0.064 2.00e-02 2.50e+03   4.21e-02 4.43e+01
        pdb=" N1   DT I  89 "   -0.102 2.00e-02 2.50e+03
        pdb=" C2   DT I  89 "    0.048 2.00e-02 2.50e+03
        pdb=" O2   DT I  89 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DT I  89 "   -0.010 2.00e-02 2.50e+03
        pdb=" C4   DT I  89 "    0.007 2.00e-02 2.50e+03
        pdb=" O4   DT I  89 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DT I  89 "    0.016 2.00e-02 2.50e+03
        pdb=" C7   DT I  89 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DT I  89 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1344 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 40
        2.54 -     3.13: 8386
        3.13 -     3.72: 21654
        3.72 -     4.31: 28955
        4.31 -     4.90: 42283
  Nonbonded interactions: 101318
  Sorted by model distance:
  nonbonded pdb=" O5'  DA I  90 "
            pdb=" O4'  DA I  90 "
     model   vdw
     1.947 2.432
  nonbonded pdb=" O4'  DT I  89 "
            pdb=" C2   DT I  89 "
     model   vdw
     2.120 2.608
  nonbonded pdb=" C1'  DT I  89 "
            pdb=" O2   DT I  89 "
     model   vdw
     2.194 2.776
  nonbonded pdb=" OE2 GLU E  73 "
            pdb=" ND2 ASN F  25 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O4'  DT I  89 "
            pdb=" O2   DT I  89 "
     model   vdw
     2.206 3.040
  ... (remaining 101313 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 40 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and ((resid 19 through 20 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 24 through 101))
  selection = (chain 'F' and resid 19 through 101)
}
ncs_group {
  reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 75 through 118))
  selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 37 through 118))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 56 through 121))
}

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:             1.030
  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:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.330
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
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      :  0.013   0.388  12843  Z= 1.106
  Angle     :  1.101  20.866  18610  Z= 0.930
  Chirality :  0.065   0.782   2127
  Planarity :  0.006   0.068   1347
  Dihedral  : 27.916 175.925   5523
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.64 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.89 (0.30), residues: 751
  helix:  2.82 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.54 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.037   0.001   ARG B  19 
 TYR   0.018   0.002   TYR B  88 
 PHE   0.012   0.001   PHE D  67 
 HIS   0.006   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01276 /  1.11 (12843)
  covalent geometry    : angle       1.10065 /  0.93 (18610)
  hydrogen bonds       : bond        0.10856 /  7.25 (  757)
  hydrogen bonds       : angle       3.37182 /  2.51 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7865 (mt) cc_final: 0.7564 (mt)
REVERT: C   41 GLU cc_start: 0.7525 (tt0) cc_final: 0.7219 (tt0)
REVERT: C   99 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8032 (mmm160)
REVERT: D   39 TYR cc_start: 0.8208 (t80) cc_final: 0.7931 (t80)
REVERT: D   48 ASP cc_start: 0.8250 (p0) cc_final: 0.8002 (p0)
REVERT: D   73 GLU cc_start: 0.8095 (tp30) cc_final: 0.7815 (tp30)
REVERT: D   82 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8498 (mmtt)
REVERT: D  102 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7925 (mt-10)
REVERT: G   90 ASP cc_start: 0.8076 (t0) cc_final: 0.7660 (t0)
REVERT: G   95 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8672 (ttmm)
REVERT: H   36 ILE cc_start: 0.8634 (mt) cc_final: 0.8324 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1502
  time to fit residues: 37.1008
Evaluate side-chains
  127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0870
   overall best weight:    0.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
B  93 GLN
C  24 GLN
E  76 GLN
F  75 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.080173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.058148 restraints weight = 48546.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.32
r_work: 0.3060 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  12843  Z= 0.162
  Angle     :  0.666  10.209  18610  Z= 0.396
  Chirality :  0.047   0.358   2127
  Planarity :  0.005   0.039   1347
  Dihedral  : 30.937 167.785   4045
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.92 %
    Favored  : 89.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.97 (0.30), residues: 751
  helix:  2.87 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.60 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  96 
 TYR   0.008   0.001   TYR H  80 
 PHE   0.007   0.001   PHE H  67 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.16 (12843)
  covalent geometry    : angle       0.66600 /  0.40 (18610)
  hydrogen bonds       : bond        0.06281 /  4.19 (  757)
  hydrogen bonds       : angle       3.01197 /  2.17 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8395 (pm20) cc_final: 0.8189 (pm20)
REVERT: A  120 MET cc_start: 0.8588 (mmm) cc_final: 0.8375 (mmm)
REVERT: A  125 GLN cc_start: 0.9191 (mt0) cc_final: 0.8925 (mt0)
REVERT: C   56 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8643 (tt0)
REVERT: C   90 ASP cc_start: 0.9210 (t0) cc_final: 0.8946 (t0)
REVERT: D   30 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6502 (mtp180)
REVERT: D   48 ASP cc_start: 0.8454 (p0) cc_final: 0.8197 (p0)
REVERT: D   80 TYR cc_start: 0.7803 (m-10) cc_final: 0.7592 (m-10)
REVERT: E  120 MET cc_start: 0.7806 (mtt) cc_final: 0.7353 (mtt)
REVERT: G   90 ASP cc_start: 0.8665 (t0) cc_final: 0.8439 (t0)
REVERT: G   95 LYS cc_start: 0.9360 (ttmt) cc_final: 0.9158 (ttmm)
REVERT: H   76 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8537 (mtt-85)
  outliers start: 7
  outliers final: 4
  residues processed: 140
  average time/residue: 0.1273
  time to fit residues: 24.7806
Evaluate side-chains
  128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 123
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   30 ARG
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 93 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 86 optimal weight:   40.0000
   chunk 83 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A  76 GLN
B  93 GLN
H  46 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.074184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.051969 restraints weight = 48223.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.33
r_work: 0.2878 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  12843  Z= 0.211
  Angle     :  0.686   8.186  18610  Z= 0.396
  Chirality :  0.048   0.336   2127
  Planarity :  0.005   0.037   1347
  Dihedral  : 31.385 165.805   4045
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.51 %
    Favored  : 88.06 %
  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:  2.79 (0.30), residues: 751
  helix:  2.76 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.80 (0.39), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  89 
 TYR   0.013   0.002   TYR D  37 
 PHE   0.015   0.002   PHE C  25 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.21 (12843)
  covalent geometry    : angle       0.68616 /  0.40 (18610)
  hydrogen bonds       : bond        0.06380 /  4.35 (  757)
  hydrogen bonds       : angle       2.97978 /  2.11 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8559 (pm20) cc_final: 0.8105 (pm20)
REVERT: A  120 MET cc_start: 0.8795 (mmm) cc_final: 0.8473 (mmm)
REVERT: A  125 GLN cc_start: 0.9256 (mt0) cc_final: 0.9009 (mt0)
REVERT: C   56 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8717 (tt0)
REVERT: D   30 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7205 (mtp180)
REVERT: D   48 ASP cc_start: 0.8584 (p0) cc_final: 0.8297 (p0)
REVERT: D   65 ASP cc_start: 0.9228 (t0) cc_final: 0.8956 (t0)
REVERT: D   80 TYR cc_start: 0.7916 (m-10) cc_final: 0.7627 (m-10)
REVERT: G   90 ASP cc_start: 0.8758 (t0) cc_final: 0.8541 (t0)
REVERT: H   76 ARG cc_start: 0.8834 (ttm-80) cc_final: 0.8614 (mtt-85)
  outliers start: 9
  outliers final: 6
  residues processed: 126
  average time/residue: 0.1206
  time to fit residues: 21.0638
Evaluate side-chains
  121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   30 ARG
Chi-restraints excluded: chain E residue  124 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 98 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   chunk 73 optimal weight:   20.0000
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
B  93 GLN
H  46 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.074452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.052279 restraints weight = 47903.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 2.39
r_work: 0.2891 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12843  Z= 0.148
  Angle     :  0.602   8.189  18610  Z= 0.356
  Chirality :  0.042   0.291   2127
  Planarity :  0.004   0.039   1347
  Dihedral  : 31.248 167.640   4045
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.74 %
    Favored  : 85.67 %
  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:  3.17 (0.31), residues: 751
  helix:  3.07 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.73 (0.39), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  29 
 TYR   0.013   0.001   TYR D  34 
 PHE   0.011   0.001   PHE C  25 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.15 (12843)
  covalent geometry    : angle       0.60202 /  0.36 (18610)
  hydrogen bonds       : bond        0.04712 /  3.19 (  757)
  hydrogen bonds       : angle       2.77233 /  1.96 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8563 (pm20) cc_final: 0.8181 (pm20)
REVERT: A  120 MET cc_start: 0.8691 (mmm) cc_final: 0.8371 (mmm)
REVERT: A  125 GLN cc_start: 0.9222 (mt0) cc_final: 0.8963 (mt0)
REVERT: C   56 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8737 (tt0)
REVERT: D   30 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7160 (mtp180)
REVERT: D   48 ASP cc_start: 0.8593 (p0) cc_final: 0.8277 (p0)
REVERT: D   65 ASP cc_start: 0.9209 (t0) cc_final: 0.8949 (t0)
REVERT: D   80 TYR cc_start: 0.7929 (m-10) cc_final: 0.7662 (m-10)
REVERT: F   24 ASP cc_start: 0.6842 (t0) cc_final: 0.6605 (t0)
REVERT: H   76 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8569 (mtt-85)
  outliers start: 10
  outliers final: 6
  residues processed: 127
  average time/residue: 0.1231
  time to fit residues: 21.9122
Evaluate side-chains
  121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   30 ARG
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 99 optimal weight:   30.0000
   chunk 40 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 74 optimal weight:   30.0000
   chunk 36 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.071921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.049934 restraints weight = 47934.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.39
r_work: 0.2838 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12843  Z= 0.178
  Angle     :  0.639   9.053  18610  Z= 0.370
  Chirality :  0.044   0.289   2127
  Planarity :  0.004   0.038   1347
  Dihedral  : 31.233 166.714   4045
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.78 %
    Favored  : 85.51 %
  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:  3.01 (0.30), residues: 751
  helix:  2.94 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.79 (0.39), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  72 
 TYR   0.014   0.002   TYR D  34 
 PHE   0.016   0.002   PHE C  25 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.18 (12843)
  covalent geometry    : angle       0.63925 /  0.37 (18610)
  hydrogen bonds       : bond        0.05535 /  3.74 (  757)
  hydrogen bonds       : angle       2.81308 /  1.99 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8250 (pm20)
REVERT: A  120 MET cc_start: 0.8790 (mmm) cc_final: 0.8459 (mmm)
REVERT: A  125 GLN cc_start: 0.9265 (mt0) cc_final: 0.9019 (mt0)
REVERT: C   56 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8594 (tm-30)
REVERT: D   30 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7266 (mtp180)
REVERT: D   48 ASP cc_start: 0.8646 (p0) cc_final: 0.8341 (p0)
REVERT: D   65 ASP cc_start: 0.9222 (t0) cc_final: 0.8938 (t0)
REVERT: D   80 TYR cc_start: 0.8150 (m-10) cc_final: 0.7774 (m-10)
REVERT: E   59 GLU cc_start: 0.8947 (pm20) cc_final: 0.8734 (pm20)
REVERT: G   90 ASP cc_start: 0.8960 (t0) cc_final: 0.8746 (t0)
REVERT: H   76 ARG cc_start: 0.8954 (ttm-80) cc_final: 0.8637 (mtt-85)
  outliers start: 17
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1131
  time to fit residues: 19.9051
Evaluate side-chains
  127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   30 ARG
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 82 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 87 optimal weight:   30.0000
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 113 HIS
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.072305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.050432 restraints weight = 48205.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 2.39
r_work: 0.2849 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12843  Z= 0.142
  Angle     :  0.595   8.881  18610  Z= 0.350
  Chirality :  0.041   0.285   2127
  Planarity :  0.004   0.038   1347
  Dihedral  : 31.170 167.819   4045
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.42 %
    Favored  : 85.35 %
  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:  3.23 (0.31), residues: 751
  helix:  3.14 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.81 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  29 
 TYR   0.012   0.001   TYR D  34 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.14 (12843)
  covalent geometry    : angle       0.59484 /  0.35 (18610)
  hydrogen bonds       : bond        0.04470 /  3.02 (  757)
  hydrogen bonds       : angle       2.70413 /  1.91 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8241 (pm20)
REVERT: A  120 MET cc_start: 0.8668 (mmm) cc_final: 0.8328 (mmm)
REVERT: A  125 GLN cc_start: 0.9241 (mt0) cc_final: 0.8987 (mt0)
REVERT: B   78 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8492 (mtm-85)
REVERT: C   56 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8731 (tt0)
REVERT: D   30 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7223 (mtp180)
REVERT: D   48 ASP cc_start: 0.8671 (p0) cc_final: 0.8360 (p0)
REVERT: D   65 ASP cc_start: 0.9207 (t0) cc_final: 0.8943 (t0)
REVERT: D   80 TYR cc_start: 0.8011 (m-10) cc_final: 0.7678 (m-10)
REVERT: E  120 MET cc_start: 0.7934 (mtt) cc_final: 0.7650 (mtt)
REVERT: F   24 ASP cc_start: 0.6045 (t0) cc_final: 0.5825 (t0)
REVERT: H   76 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8644 (mtt-85)
  outliers start: 14
  outliers final: 9
  residues processed: 126
  average time/residue: 0.1100
  time to fit residues: 19.4455
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   30 ARG
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 99 optimal weight:   30.0000
   chunk 91 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 84 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 72 optimal weight:   40.0000
   chunk 43 optimal weight:    0.8980
   chunk 95 optimal weight:   20.0000
   chunk 80 optimal weight:   10.0000
   chunk 4 optimal weight:    0.6980
   overall best weight:    3.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.068618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.046833 restraints weight = 47698.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 2.36
r_work: 0.2749 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.4111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  12843  Z= 0.283
  Angle     :  0.744  13.239  18610  Z= 0.416
  Chirality :  0.047   0.297   2127
  Planarity :  0.005   0.040   1347
  Dihedral  : 31.438 162.736   4045
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.10 %
    Favored  : 85.51 %
  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:  2.71 (0.30), residues: 751
  helix:  2.76 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.02 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  89 
 TYR   0.018   0.002   TYR D  34 
 PHE   0.019   0.002   PHE C  25 
 HIS   0.005   0.002   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00588 /  0.28 (12843)
  covalent geometry    : angle       0.74412 /  0.42 (18610)
  hydrogen bonds       : bond        0.06733 /  4.53 (  757)
  hydrogen bonds       : angle       3.04282 /  2.15 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8780 (pm20) cc_final: 0.8280 (pm20)
REVERT: A  120 MET cc_start: 0.8811 (mmm) cc_final: 0.8448 (mmm)
REVERT: C   56 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8660 (tm-30)
REVERT: D   30 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7323 (mtp180)
REVERT: D   48 ASP cc_start: 0.8719 (p0) cc_final: 0.8397 (p0)
REVERT: D   65 ASP cc_start: 0.9252 (t0) cc_final: 0.8976 (t0)
REVERT: D   80 TYR cc_start: 0.8085 (m-10) cc_final: 0.7733 (m-10)
REVERT: H   76 ARG cc_start: 0.8971 (ttm-80) cc_final: 0.8660 (mtt-85)
  outliers start: 15
  outliers final: 10
  residues processed: 123
  average time/residue: 0.1269
  time to fit residues: 21.4172
Evaluate side-chains
  122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   30 ARG
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 88 optimal weight:   20.0000
   chunk 64 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A 125 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.069989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.048430 restraints weight = 47842.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.34
r_work: 0.2803 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12843  Z= 0.140
  Angle     :  0.611  10.676  18610  Z= 0.356
  Chirality :  0.041   0.281   2127
  Planarity :  0.004   0.035   1347
  Dihedral  : 31.254 165.938   4045
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.38 %
    Favored  : 85.03 %
  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:  3.08 (0.31), residues: 751
  helix:  3.04 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.91 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  96 
 TYR   0.014   0.001   TYR D  34 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.14 (12843)
  covalent geometry    : angle       0.61109 /  0.36 (18610)
  hydrogen bonds       : bond        0.04378 /  2.94 (  757)
  hydrogen bonds       : angle       2.76339 /  1.95 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8677 (pm20) cc_final: 0.8302 (pm20)
REVERT: A  120 MET cc_start: 0.8686 (mmm) cc_final: 0.8300 (mmm)
REVERT: C   56 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8674 (tm-30)
REVERT: D   48 ASP cc_start: 0.8765 (p0) cc_final: 0.8469 (p0)
REVERT: D   65 ASP cc_start: 0.9204 (t0) cc_final: 0.8994 (t0)
REVERT: D   80 TYR cc_start: 0.8056 (m-10) cc_final: 0.7793 (m-10)
REVERT: H   31 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8411 (mptt)
REVERT: H   76 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8607 (mtt-85)
  outliers start: 10
  outliers final: 6
  residues processed: 122
  average time/residue: 0.1168
  time to fit residues: 19.9147
Evaluate side-chains
  121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 75 optimal weight:   20.0000
   chunk 59 optimal weight:    0.3980
   chunk 34 optimal weight:    5.9990
   chunk 94 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 89 optimal weight:   20.0000
   chunk 56 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.068929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.047454 restraints weight = 48206.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.31
r_work: 0.2775 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12843  Z= 0.181
  Angle     :  0.634  11.290  18610  Z= 0.365
  Chirality :  0.043   0.279   2127
  Planarity :  0.004   0.038   1347
  Dihedral  : 31.237 164.962   4045
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.54 %
    Favored  : 85.19 %
  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:  3.02 (0.31), residues: 751
  helix:  3.00 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.94 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  77 
 TYR   0.014   0.001   TYR D  34 
 PHE   0.012   0.002   PHE C  25 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.18 (12843)
  covalent geometry    : angle       0.63410 /  0.37 (18610)
  hydrogen bonds       : bond        0.05093 /  3.44 (  757)
  hydrogen bonds       : angle       2.82663 /  2.00 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8322 (pm20)
REVERT: A  120 MET cc_start: 0.8689 (mmm) cc_final: 0.8316 (mmm)
REVERT: B   88 TYR cc_start: 0.9260 (m-10) cc_final: 0.8572 (m-10)
REVERT: C   56 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8647 (tm-30)
REVERT: D   48 ASP cc_start: 0.8753 (p0) cc_final: 0.8468 (p0)
REVERT: D   65 ASP cc_start: 0.9261 (t0) cc_final: 0.8983 (t0)
REVERT: D   80 TYR cc_start: 0.8100 (m-10) cc_final: 0.7816 (m-10)
REVERT: D  102 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8282 (tt0)
REVERT: H   31 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8472 (mptt)
REVERT: H   76 ARG cc_start: 0.8953 (ttm-80) cc_final: 0.8629 (mtt-85)
  outliers start: 8
  outliers final: 6
  residues processed: 117
  average time/residue: 0.1200
  time to fit residues: 19.4785
Evaluate side-chains
  121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 99 optimal weight:   30.0000
   chunk 92 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0050
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 83 optimal weight:   20.0000
   overall best weight:    0.9198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.069680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.048349 restraints weight = 48094.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.29
r_work: 0.2807 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12843  Z= 0.135
  Angle     :  0.596  11.739  18610  Z= 0.350
  Chirality :  0.040   0.277   2127
  Planarity :  0.004   0.036   1347
  Dihedral  : 31.115 166.320   4045
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.54 %
    Favored  : 85.19 %
  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:  3.14 (0.31), residues: 751
  helix:  3.09 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.90 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  96 
 TYR   0.012   0.001   TYR D  34 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.13 (12843)
  covalent geometry    : angle       0.59580 /  0.35 (18610)
  hydrogen bonds       : bond        0.04072 /  2.75 (  757)
  hydrogen bonds       : angle       2.70271 /  1.92 ( 1911)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8276 (pm20)
REVERT: A  120 MET cc_start: 0.8635 (mmm) cc_final: 0.8239 (mmm)
REVERT: B   78 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8563 (mtm-85)
REVERT: C   56 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8622 (tm-30)
REVERT: D   48 ASP cc_start: 0.8697 (p0) cc_final: 0.8416 (p0)
REVERT: D   65 ASP cc_start: 0.9212 (t0) cc_final: 0.8962 (t0)
REVERT: D   80 TYR cc_start: 0.8012 (m-10) cc_final: 0.7777 (m-10)
REVERT: D  102 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8253 (tt0)
REVERT: H   31 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8490 (mptt)
REVERT: H   76 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8582 (mtt-85)
  outliers start: 8
  outliers final: 4
  residues processed: 123
  average time/residue: 0.1240
  time to fit residues: 21.3164
Evaluate side-chains
  125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   25 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.069705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.048373 restraints weight = 47655.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.32
r_work: 0.2809 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.4326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.115  12843  Z= 0.193
  Angle     :  0.826  59.157  18610  Z= 0.503
  Chirality :  0.042   0.600   2127
  Planarity :  0.004   0.065   1347
  Dihedral  : 31.116 166.285   4045
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 14.49 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  3.15 (0.31), residues: 751
  helix:  3.09 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.90 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.000   ARG D  30 
 TYR   0.016   0.001   TYR G  57 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.002   0.000   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.19 (12843)
  covalent geometry    : angle       0.82641 /  0.50 (18610)
  hydrogen bonds       : bond        0.04078 /  2.75 (  757)
  hydrogen bonds       : angle       2.70062 /  1.91 ( 1911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2471.63 seconds
wall clock time: 43 minutes 2.57 seconds (2582.57 seconds total)