Starting phenix.real_space_refine
on Wed Aug  5 01:36:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u5p_63878/08_2026/9u5p_63878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u5p_63878/08_2026/9u5p_63878.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u5p_63878/08_2026/9u5p_63878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u5p_63878/08_2026/9u5p_63878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u5p_63878/08_2026/9u5p_63878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u5p_63878/08_2026/9u5p_63878.cif"
  }
  resolution = 2.96
  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=   0.007 sd=   1.046
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      75      5.49       5
     S      30      5.16       5
     C    4667      2.51       5
     N    1359      2.21       5
     O    1756      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 7887
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1391
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 5, 'TRANS': 174}
    Chain: "B"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 973
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
    Chain: "C"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 780
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 7, 'TRANS': 97}
    Chain: "O"
      Number of atoms: 1391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1391
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 5, 'TRANS': 174}
    Chain: "P"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 973
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
    Chain: "Q"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 792
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    Chain: "R"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1587
          Classifications: {'RNA': 75}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36}
          Link IDs: {'rna2p': 8, 'rna3p': 66}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.25, per 1000 atoms: 0.29
  Number of scatterers: 7887
  At special positions: 0
  Unit cell: (85.44, 106.56, 133.44, 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      30     16.00
     P      75     15.00
     O    1756      8.00
     N    1359      7.00
     C    4667      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: 0.78
  Conformation dependent library (CDL) restraints added in 483.3 milliseconds
  

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1466

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 16 sheets defined
      10.2% alpha, 44.2% beta
      25 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 14
    Processing helix  chain 'A' and resid 38 through 42
    Processing helix  chain 'A' and resid 86 through 90
      removed outlier: 3.686A  pdb=" N   ILE A  90 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.775A  pdb=" N   GLN A 145 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   CYS A 146 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 142 through 146'
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.558A  pdb=" N   TYR A 177 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE A 178 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 174 through 178'
    Processing helix  chain 'B' and resid 30 through 34
      removed outlier: 3.622A  pdb=" N   SER B  33 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   TYR B  34 " --> pdb=" O   PHE B  31 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 30 through 34'
    Processing helix  chain 'C' and resid 26 through 30
      removed outlier: 3.642A  pdb=" N   ASP C  29 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 82
      removed outlier: 3.798A  pdb=" N   ASP C  81 " --> pdb=" O   GLN C  78 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU C  82 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 78 through 82'
    Processing helix  chain 'O' and resid 3 through 14
      removed outlier: 3.892A  pdb=" N   SER O   9 " --> pdb=" O   GLU O   5 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 38 through 42
    Processing helix  chain 'O' and resid 86 through 90
      removed outlier: 3.837A  pdb=" N   ILE O  90 " --> pdb=" O   ARG O  87 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 30 through 34
      removed outlier: 3.867A  pdb=" N   SER P  33 " --> pdb=" O   THR P  30 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   TYR P  34 " --> pdb=" O   PHE P  31 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 30 through 34'
    Processing helix  chain 'P' and resid 89 through 93
      removed outlier: 4.099A  pdb=" N   THR P  93 " --> pdb=" O   ALA P  90 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 26 through 30
      removed outlier: 3.513A  pdb=" N   ASP Q  29 " --> pdb=" O   LYS Q  26 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20
      removed outlier: 3.520A  pdb=" N   LEU A  28 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL A  34 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   LEU A  72 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASP A  58 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASP A  78 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   VAL A  56 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 126
      removed outlier: 6.980A  pdb=" N   MET A 120 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ILE A 135 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   GLY A 122 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ARG A 133 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   ARG A 133 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   ALA A 171 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   HIS A 160 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU A 150 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ALA A  99 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL A 115 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   SER A 105 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   THR A 109 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 10
    Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14
      removed outlier: 3.651A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 123 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR B 125 " --> pdb=" O   GLY B  12 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ARG B  40 " --> pdb=" O   TRP B  49 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   TRP B  49 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 14
      removed outlier: 3.651A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 123 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR B 125 " --> pdb=" O   GLY B  12 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   VAL B 117 " --> pdb=" O   ARG B 100 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 11
      removed outlier: 3.596A  pdb=" N   THR C 104 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23
    Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47
      removed outlier: 6.848A  pdb=" N   TRP C  34 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR C  94 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'O' and resid 15 through 20
      removed outlier: 3.701A  pdb=" N   LEU O  28 " --> pdb=" O   VAL O  36 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   VAL O  34 " --> pdb=" O   ILE O  30 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   LEU O  72 " --> pdb=" O   LEU O  62 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASP O  58 " --> pdb=" O   THR O  76 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'O' and resid 119 through 120
      removed outlier: 5.885A  pdb=" N   ALA O 171 " --> pdb=" O   HIS O 160 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   HIS O 160 " --> pdb=" O   ALA O 171 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   ILE O 156 " --> pdb=" O   ALA O 152 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ALA O 152 " --> pdb=" O   ILE O 156 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY O 158 " --> pdb=" O   LEU O 150 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA O  99 " --> pdb=" O   VAL O 115 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL O 115 " --> pdb=" O   ALA O  99 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   SER O 105 " --> pdb=" O   THR O 109 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR O 109 " --> pdb=" O   SER O 105 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'O' and resid 124 through 125
    Processing sheet with id=AB3, first strand: chain 'P' and resid 5 through 10
    Processing sheet with id=AB4, first strand: chain 'P' and resid 13 through 14
      removed outlier: 6.837A  pdb=" N   MET P  36 " --> pdb=" O   VAL P  52 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   VAL P  52 " --> pdb=" O   MET P  36 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   TRP P  38 " --> pdb=" O   VAL P  50 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'Q' and resid 4 through 5
    Processing sheet with id=AB6, first strand: chain 'Q' and resid 9 through 12
      removed outlier: 3.504A  pdb=" N   THR Q 104 " --> pdb=" O   VAL Q  10 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   VAL Q  12 " --> pdb=" O   THR Q 104 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'Q' and resid 44 through 47
      removed outlier: 6.870A  pdb=" N   TRP Q  34 " --> pdb=" O   VAL Q  46 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   TYR Q  31 " --> pdb=" O   TRP Q  90 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TRP Q  90 " --> pdb=" O   TYR Q  31 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    603 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      64 hydrogen bonds
      120 hydrogen bond angles
      0 basepair planarities
      25 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2247
        1.34 -     1.45: 1751
        1.45 -     1.57: 4003
        1.57 -     1.69: 148
        1.69 -     1.81: 44
  Bond restraints: 8193
  Sorted by residual:
  bond pdb=" P     A R  13 "
       pdb=" O5'   A R  13 "
    ideal  model  delta    sigma   weight residual
    1.593  1.620 -0.027 1.00e-02 1.00e+04 7.16e+00
  bond pdb=" P     G R  12 "
       pdb=" O5'   G R  12 "
    ideal  model  delta    sigma   weight residual
    1.593  1.616 -0.023 1.00e-02 1.00e+04 5.46e+00
  bond pdb=" P     A R  13 "
       pdb=" OP2   A R  13 "
    ideal  model  delta    sigma   weight residual
    1.485  1.527 -0.042 2.00e-02 2.50e+03 4.40e+00
  bond pdb=" P     G R  12 "
       pdb=" OP2   G R  12 "
    ideal  model  delta    sigma   weight residual
    1.485  1.527 -0.042 2.00e-02 2.50e+03 4.38e+00
  bond pdb=" N   ARG O  87 "
       pdb=" CA  ARG O  87 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.028 1.33e-02 5.65e+03 4.33e+00
  ... (remaining 8188 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 11065
        1.86 -     3.71: 336
        3.71 -     5.57: 38
        5.57 -     7.42: 6
        7.42 -     9.28: 2
  Bond angle restraints: 11447
  Sorted by residual:
  angle pdb=" C3'   U R  14 "
        pdb=" O3'   U R  14 "
        pdb=" P     G R  15 "
      ideal   model   delta    sigma   weight residual
     119.70  124.30   -4.60 1.20e+00 6.94e-01 1.47e+01
  angle pdb=" C1'   C R  57 "
        pdb=" N1    C R  57 "
        pdb=" C2    C R  57 "
      ideal   model   delta    sigma   weight residual
     118.80  122.62   -3.82 1.10e+00 8.26e-01 1.21e+01
  angle pdb=" CB  MET O 134 "
        pdb=" CG  MET O 134 "
        pdb=" SD  MET O 134 "
      ideal   model   delta    sigma   weight residual
     112.70  103.42    9.28 3.00e+00 1.11e-01 9.57e+00
  angle pdb=" CA  THR C 104 "
        pdb=" C   THR C 104 "
        pdb=" O   THR C 104 "
      ideal   model   delta    sigma   weight residual
     120.36  123.66   -3.30 1.08e+00 8.57e-01 9.33e+00
  angle pdb=" C2'   A R  56 "
        pdb=" C1'   A R  56 "
        pdb=" N9    A R  56 "
      ideal   model   delta    sigma   weight residual
     112.00  115.32   -3.32 1.10e+00 8.26e-01 9.13e+00
  ... (remaining 11442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.94: 4422
       22.94 -    45.88: 358
       45.88 -    68.83: 152
       68.83 -    91.77: 26
       91.77 -   114.71: 1
  Dihedral angle restraints: 4959
    sinusoidal: 2635
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" O4'   A R   4 "
           pdb=" C1'   A R   4 "
           pdb=" N9    A R   4 "
           pdb=" C4    A R   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -154.66   48.66     1      1.70e+01 3.46e-03 1.13e+01
  dihedral pdb=" C4'   U R  14 "
           pdb=" C3'   U R  14 "
           pdb=" O3'   U R  14 "
           pdb=" P     G R  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00  105.29  114.71     1      3.50e+01 8.16e-04 1.11e+01
  dihedral pdb=" CG  ARG A  79 "
           pdb=" CD  ARG A  79 "
           pdb=" NE  ARG A  79 "
           pdb=" CZ  ARG A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.93  -44.93     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 4956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 1147
       0.101 -    0.203: 185
       0.203 -    0.304: 3
       0.304 -    0.405: 4
       0.405 -    0.507: 5
  Chirality restraints: 1344
  Sorted by residual:
  chirality pdb=" P     C R  82 "
            pdb=" OP1   C R  82 "
            pdb=" OP2   C R  82 "
            pdb=" O5'   C R  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.92   -0.51 2.00e-01 2.50e+01 6.42e+00
  chirality pdb=" P     A R   4 "
            pdb=" OP1   A R   4 "
            pdb=" OP2   A R   4 "
            pdb=" O5'   A R   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.90   -0.49 2.00e-01 2.50e+01 6.06e+00
  chirality pdb=" P     C R  25 "
            pdb=" OP1   C R  25 "
            pdb=" OP2   C R  25 "
            pdb=" O5'   C R  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.89   -0.48 2.00e-01 2.50e+01 5.69e+00
  ... (remaining 1341 not shown)

  Planarity restraints: 1193
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C   7 "   -0.042 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO C   8 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C   8 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C   8 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE O  37 "   -0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO O  38 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO O  38 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO O  38 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  71 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   GLU A  71 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLU A  71 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A  72 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1190 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1187
        2.76 -     3.30: 6459
        3.30 -     3.83: 12638
        3.83 -     4.37: 15177
        4.37 -     4.90: 25682
  Nonbonded interactions: 61143
  Sorted by model distance:
  nonbonded pdb=" O2'   U R  14 "
            pdb=" OP1   G R  15 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   SER P  54 "
            pdb=" NH1 ARG P  74 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" NH1 ARG O 133 "
            pdb=" OH  TYR O 177 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" OP2   C R  10 "
            pdb=" O2'   U R  42 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OH  TYR C   2 "
            pdb=" O   ASP C  25 "
     model   vdw
     2.344 3.040
  ... (remaining 61138 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'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'Q' and resid 1 through 105)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.070
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.550
  Find NCS groups from input model:        0.110
  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:7.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
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   0.042   8193  Z= 0.311
  Angle     :  0.719   9.281  11447  Z= 0.439
  Chirality :  0.072   0.507   1344
  Planarity :  0.004   0.064   1193
  Dihedral  : 18.724 114.709   3493
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.85 %
    Favored  : 82.15 %
  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:  0.07 (0.30), residues: 814
  helix:  0.62 (1.30), residues: 22
  sheet:  0.85 (0.28), residues: 373
  loop : -0.73 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 136 
 TYR   0.010   0.001   TYR B  97 
 PHE   0.011   0.001   PHE B  70 
 TRP   0.011   0.001   TRP C  90 
 HIS   0.003   0.001   HIS O 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.31 ( 8193)
  covalent geometry    : angle       0.71942 /  0.44 (11447)
  hydrogen bonds       : bond        0.15859 / 10.29 (  302)
  hydrogen bonds       : angle       5.50760 /  3.99 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.8600 (mtt90) cc_final: 0.8393 (mtt180)
REVERT: A   75 LEU cc_start: 0.7622 (mt) cc_final: 0.7274 (mp)
REVERT: A   78 ASP cc_start: 0.8035 (t0) cc_final: 0.7749 (t0)
REVERT: A  123 LEU cc_start: 0.8212 (tt) cc_final: 0.8008 (tt)
REVERT: A  124 ILE cc_start: 0.7868 (mm) cc_final: 0.7574 (mp)
REVERT: A  143 THR cc_start: 0.8618 (m) cc_final: 0.8399 (p)
REVERT: B   33 SER cc_start: 0.7956 (m) cc_final: 0.7673 (p)
REVERT: B   60 LYS cc_start: 0.8816 (mttt) cc_final: 0.8492 (mttm)
REVERT: B   89 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7597 (mtm110)
REVERT: P    9 SER cc_start: 0.7899 (t) cc_final: 0.7668 (t)
REVERT: P   36 MET cc_start: 0.8599 (mmt) cc_final: 0.8348 (mmm)
REVERT: P   62 TYR cc_start: 0.8708 (m-80) cc_final: 0.8475 (m-80)
REVERT: P   73 SER cc_start: 0.8395 (t) cc_final: 0.8151 (t)
REVERT: P   87 SER cc_start: 0.8733 (m) cc_final: 0.8207 (p)
REVERT: P  106 TYR cc_start: 0.8936 (p90) cc_final: 0.8564 (p90)
REVERT: P  115 MET cc_start: 0.8375 (mmt) cc_final: 0.7509 (mpt)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.3795
  time to fit residues: 51.2929
Evaluate side-chains
  100 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
B   8 GLN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.126342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.098293 restraints weight = 10916.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.62
r_work: 0.3110 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.0740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8193  Z= 0.124
  Angle     :  0.515   6.440  11447  Z= 0.285
  Chirality :  0.041   0.257   1344
  Planarity :  0.004   0.050   1193
  Dihedral  : 18.179 119.011   2071
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 19.01 %
    Favored  : 79.68 %
  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:  0.08 (0.30), residues: 814
  helix:  0.89 (1.17), residues: 22
  sheet:  0.84 (0.28), residues: 371
  loop : -0.72 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  74 
 TYR   0.011   0.001   TYR B  97 
 PHE   0.012   0.001   PHE P  31 
 TRP   0.013   0.001   TRP C  90 
 HIS   0.004   0.001   HIS O  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 8193)
  covalent geometry    : angle       0.51547 /  0.28 (11447)
  hydrogen bonds       : bond        0.05198 /  3.42 (  302)
  hydrogen bonds       : angle       4.83443 /  3.42 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8573 (mtt180)
REVERT: A   70 LEU cc_start: 0.8770 (mt) cc_final: 0.8536 (mp)
REVERT: A   78 ASP cc_start: 0.8174 (t0) cc_final: 0.7933 (t0)
REVERT: A  123 LEU cc_start: 0.8490 (tt) cc_final: 0.8248 (tt)
REVERT: A  124 ILE cc_start: 0.8327 (mm) cc_final: 0.8052 (mp)
REVERT: B   60 LYS cc_start: 0.8969 (mttt) cc_final: 0.8749 (mttm)
REVERT: B   87 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8243 (p)
REVERT: P   62 TYR cc_start: 0.8708 (m-80) cc_final: 0.8487 (m-80)
REVERT: P   73 SER cc_start: 0.8419 (t) cc_final: 0.8191 (t)
REVERT: P   87 SER cc_start: 0.8768 (m) cc_final: 0.8291 (p)
  outliers start: 9
  outliers final: 5
  residues processed: 110
  average time/residue: 0.3966
  time to fit residues: 46.5072
Evaluate side-chains
  99 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue  176 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0020
   chunk 49 optimal weight:    0.4980
   chunk 47 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
B   8 GLN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.126458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.098307 restraints weight = 10927.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.62
r_work: 0.3118 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8193  Z= 0.114
  Angle     :  0.484   5.571  11447  Z= 0.268
  Chirality :  0.040   0.263   1344
  Planarity :  0.004   0.054   1193
  Dihedral  : 18.111 121.899   2071
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.58 %
    Favored  : 79.25 %
  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:  0.10 (0.30), residues: 814
  helix:  1.06 (1.16), residues: 22
  sheet:  0.85 (0.28), residues: 367
  loop : -0.69 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  74 
 TYR   0.020   0.001   TYR O  60 
 PHE   0.010   0.001   PHE O   6 
 TRP   0.012   0.001   TRP C  90 
 HIS   0.003   0.001   HIS O 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 ( 8193)
  covalent geometry    : angle       0.48401 /  0.27 (11447)
  hydrogen bonds       : bond        0.04743 /  3.04 (  302)
  hydrogen bonds       : angle       4.58442 /  3.24 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.8825 (mtt90) cc_final: 0.8561 (mtt180)
REVERT: A   78 ASP cc_start: 0.8190 (t0) cc_final: 0.7919 (t0)
REVERT: B   60 LYS cc_start: 0.8972 (mttt) cc_final: 0.8752 (mttm)
REVERT: O  175 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8737 (mttm)
REVERT: P   62 TYR cc_start: 0.8726 (m-80) cc_final: 0.8481 (m-80)
REVERT: P   73 SER cc_start: 0.8416 (t) cc_final: 0.8185 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 118
  average time/residue: 0.4503
  time to fit residues: 56.6656
Evaluate side-chains
  116 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue  176 GLN
Chi-restraints excluded: chain P residue   65 SER
Chi-restraints excluded: chain Q residue   64 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
B   8 GLN
O  67 ASN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.125736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.097673 restraints weight = 11042.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.63
r_work: 0.3102 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8193  Z= 0.148
  Angle     :  0.510   7.889  11447  Z= 0.282
  Chirality :  0.042   0.264   1344
  Planarity :  0.004   0.057   1193
  Dihedral  : 18.051 124.320   2071
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.88 %
    Favored  : 78.23 %
  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:  0.03 (0.29), residues: 814
  helix:  1.01 (1.16), residues: 22
  sheet:  0.81 (0.27), residues: 367
  loop : -0.74 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  74 
 TYR   0.017   0.002   TYR O  60 
 PHE   0.011   0.002   PHE O   6 
 TRP   0.014   0.002   TRP C  90 
 HIS   0.004   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 8193)
  covalent geometry    : angle       0.51046 /  0.28 (11447)
  hydrogen bonds       : bond        0.04772 /  3.06 (  302)
  hydrogen bonds       : angle       4.52015 /  3.20 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   78 ASP cc_start: 0.8223 (t0) cc_final: 0.7928 (t0)
REVERT: A  124 ILE cc_start: 0.8361 (mm) cc_final: 0.8071 (mp)
REVERT: B   60 LYS cc_start: 0.8982 (mttt) cc_final: 0.8741 (mttm)
REVERT: O  175 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8732 (mttm)
REVERT: P   62 TYR cc_start: 0.8742 (m-80) cc_final: 0.8519 (m-80)
REVERT: P   73 SER cc_start: 0.8443 (t) cc_final: 0.8218 (t)
  outliers start: 13
  outliers final: 9
  residues processed: 115
  average time/residue: 0.4263
  time to fit residues: 52.5005
Evaluate side-chains
  114 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue  176 GLN
Chi-restraints excluded: chain P residue   65 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 37 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 21 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 81 optimal weight:   30.0000
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
B   8 GLN
O  67 ASN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.126300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.097562 restraints weight = 11092.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.71
r_work: 0.3099 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8193  Z= 0.131
  Angle     :  0.497   5.934  11447  Z= 0.275
  Chirality :  0.041   0.268   1344
  Planarity :  0.004   0.055   1193
  Dihedral  : 18.034 125.976   2071
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.03 %
    Favored  : 78.23 %
  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:  0.05 (0.30), residues: 814
  helix:  1.04 (1.16), residues: 22
  sheet:  0.80 (0.27), residues: 374
  loop : -0.73 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  74 
 TYR   0.019   0.001   TYR O  60 
 PHE   0.010   0.002   PHE O   6 
 TRP   0.015   0.001   TRP C  90 
 HIS   0.004   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 8193)
  covalent geometry    : angle       0.49683 /  0.28 (11447)
  hydrogen bonds       : bond        0.04563 /  2.91 (  302)
  hydrogen bonds       : angle       4.49076 /  3.18 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   78 ASP cc_start: 0.8269 (t0) cc_final: 0.7957 (t0)
REVERT: B   60 LYS cc_start: 0.8980 (mttt) cc_final: 0.8741 (mttm)
REVERT: B   77 SER cc_start: 0.8100 (m) cc_final: 0.7810 (p)
REVERT: P   62 TYR cc_start: 0.8733 (m-80) cc_final: 0.8510 (m-80)
REVERT: P   73 SER cc_start: 0.8437 (t) cc_final: 0.8059 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 110
  average time/residue: 0.5143
  time to fit residues: 60.4334
Evaluate side-chains
  108 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue   87 ARG
Chi-restraints excluded: chain O residue  176 GLN
Chi-restraints excluded: chain P residue   65 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0370
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 29 optimal weight:    0.2980
   overall best weight:    0.4658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
B   8 GLN
O  67 ASN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.126859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.098939 restraints weight = 10922.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.61
r_work: 0.3122 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8193  Z= 0.108
  Angle     :  0.486   7.757  11447  Z= 0.268
  Chirality :  0.041   0.269   1344
  Planarity :  0.004   0.054   1193
  Dihedral  : 18.018 127.335   2071
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 21.04 %
    Favored  : 77.36 %
  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:  0.11 (0.30), residues: 814
  helix:  1.14 (1.16), residues: 22
  sheet:  0.82 (0.27), residues: 374
  loop : -0.68 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  74 
 TYR   0.018   0.001   TYR O  60 
 PHE   0.009   0.001   PHE O   6 
 TRP   0.013   0.001   TRP C  90 
 HIS   0.003   0.001   HIS O 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 ( 8193)
  covalent geometry    : angle       0.48622 /  0.27 (11447)
  hydrogen bonds       : bond        0.04313 /  2.77 (  302)
  hydrogen bonds       : angle       4.40986 /  3.11 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ASP cc_start: 0.8276 (t0) cc_final: 0.7981 (t0)
REVERT: B   60 LYS cc_start: 0.8961 (mttt) cc_final: 0.8725 (mttm)
REVERT: B   77 SER cc_start: 0.8105 (m) cc_final: 0.7818 (p)
REVERT: P   73 SER cc_start: 0.8418 (t) cc_final: 0.8048 (t)
  outliers start: 11
  outliers final: 8
  residues processed: 109
  average time/residue: 0.4646
  time to fit residues: 53.9974
Evaluate side-chains
  106 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue   87 ARG
Chi-restraints excluded: chain P residue   65 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0170
   chunk 19 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0370
   chunk 15 optimal weight:    0.7980
   chunk 80 optimal weight:   20.0000
   overall best weight:    0.5096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
O  67 ASN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.127005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.099073 restraints weight = 10993.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.63
r_work: 0.3124 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8193  Z= 0.114
  Angle     :  0.487   5.790  11447  Z= 0.269
  Chirality :  0.041   0.269   1344
  Planarity :  0.004   0.056   1193
  Dihedral  : 17.999 128.621   2071
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.75 %
    Favored  : 77.36 %
  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:  0.17 (0.30), residues: 814
  helix:  1.20 (1.17), residues: 22
  sheet:  0.84 (0.28), residues: 362
  loop : -0.57 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  74 
 TYR   0.019   0.001   TYR O  60 
 PHE   0.009   0.001   PHE O   6 
 TRP   0.013   0.001   TRP C  90 
 HIS   0.003   0.001   HIS O 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 ( 8193)
  covalent geometry    : angle       0.48661 /  0.27 (11447)
  hydrogen bonds       : bond        0.04302 /  2.74 (  302)
  hydrogen bonds       : angle       4.39469 /  3.11 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8762 (mt) cc_final: 0.8525 (mp)
REVERT: A   71 GLU cc_start: 0.7297 (tt0) cc_final: 0.7006 (tt0)
REVERT: A   75 LEU cc_start: 0.7884 (mt) cc_final: 0.7545 (mp)
REVERT: A   78 ASP cc_start: 0.8286 (t0) cc_final: 0.7989 (t0)
REVERT: A  161 VAL cc_start: 0.7206 (OUTLIER) cc_final: 0.6961 (t)
REVERT: B   60 LYS cc_start: 0.8978 (mttt) cc_final: 0.8737 (mttm)
REVERT: B   77 SER cc_start: 0.8104 (m) cc_final: 0.7824 (p)
REVERT: P   73 SER cc_start: 0.8416 (t) cc_final: 0.8045 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 109
  average time/residue: 0.4997
  time to fit residues: 58.0495
Evaluate side-chains
  106 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue   87 ARG
Chi-restraints excluded: chain P residue   65 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0370
   chunk 82 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
O  67 ASN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.126761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.098820 restraints weight = 11019.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.63
r_work: 0.3122 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8193  Z= 0.124
  Angle     :  0.494   7.205  11447  Z= 0.271
  Chirality :  0.041   0.269   1344
  Planarity :  0.004   0.056   1193
  Dihedral  : 17.990 129.777   2071
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 21.04 %
    Favored  : 77.36 %
  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:  0.17 (0.29), residues: 814
  helix:  1.17 (1.17), residues: 22
  sheet:  0.79 (0.28), residues: 367
  loop : -0.54 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O 136 
 TYR   0.014   0.001   TYR O  60 
 PHE   0.010   0.002   PHE P  70 
 TRP   0.013   0.001   TRP C  90 
 HIS   0.003   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 ( 8193)
  covalent geometry    : angle       0.49363 /  0.27 (11447)
  hydrogen bonds       : bond        0.04387 /  2.79 (  302)
  hydrogen bonds       : angle       4.38405 /  3.10 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8759 (mt) cc_final: 0.8541 (mp)
REVERT: A   78 ASP cc_start: 0.8297 (t0) cc_final: 0.7998 (t0)
REVERT: B   60 LYS cc_start: 0.8985 (mttt) cc_final: 0.8742 (mttm)
REVERT: B   77 SER cc_start: 0.8106 (m) cc_final: 0.7818 (p)
REVERT: P   73 SER cc_start: 0.8430 (t) cc_final: 0.8058 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 108
  average time/residue: 0.4852
  time to fit residues: 55.8476
Evaluate side-chains
  106 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue   87 ARG
Chi-restraints excluded: chain P residue   65 SER
Chi-restraints excluded: chain Q residue   64 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0030
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
B   8 GLN
O  67 ASN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.126874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.099038 restraints weight = 10862.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.61
r_work: 0.3122 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8193  Z= 0.130
  Angle     :  0.499   6.080  11447  Z= 0.275
  Chirality :  0.041   0.269   1344
  Planarity :  0.005   0.056   1193
  Dihedral  : 17.984 130.883   2071
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 21.04 %
    Favored  : 77.21 %
  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:  0.15 (0.29), residues: 814
  helix:  1.15 (1.17), residues: 22
  sheet:  0.78 (0.28), residues: 367
  loop : -0.55 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O 136 
 TYR   0.019   0.001   TYR O  60 
 PHE   0.009   0.001   PHE O   6 
 TRP   0.013   0.001   TRP C  90 
 HIS   0.004   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 8193)
  covalent geometry    : angle       0.49883 /  0.27 (11447)
  hydrogen bonds       : bond        0.04424 /  2.81 (  302)
  hydrogen bonds       : angle       4.39070 /  3.11 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8729 (mt) cc_final: 0.8528 (mp)
REVERT: A   78 ASP cc_start: 0.8301 (t0) cc_final: 0.8017 (t0)
REVERT: B   60 LYS cc_start: 0.8985 (mttt) cc_final: 0.8740 (mttm)
REVERT: P   73 SER cc_start: 0.8440 (t) cc_final: 0.8075 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 108
  average time/residue: 0.4338
  time to fit residues: 49.9954
Evaluate side-chains
  106 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue   87 ARG
Chi-restraints excluded: chain P residue   65 SER
Chi-restraints excluded: chain Q residue   64 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 46 optimal weight:    0.3980
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0050
   chunk 18 optimal weight:    0.0570
   chunk 73 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.3712

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
O  67 ASN
O 110 ASN
O 132 ASN
P   8 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.127870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.100124 restraints weight = 10934.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.62
r_work: 0.3140 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8193  Z= 0.097
  Angle     :  0.477   6.657  11447  Z= 0.264
  Chirality :  0.041   0.268   1344
  Planarity :  0.004   0.055   1193
  Dihedral  : 17.991 131.752   2071
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 21.48 %
    Favored  : 77.21 %
  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:  0.22 (0.30), residues: 814
  helix:  1.30 (1.16), residues: 22
  sheet:  0.81 (0.28), residues: 367
  loop : -0.49 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O 136 
 TYR   0.014   0.001   TYR O  60 
 PHE   0.012   0.001   PHE P  70 
 TRP   0.014   0.001   TRP C  90 
 HIS   0.007   0.001   HIS A  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 8193)
  covalent geometry    : angle       0.47701 /  0.26 (11447)
  hydrogen bonds       : bond        0.04133 /  2.62 (  302)
  hydrogen bonds       : angle       4.36686 /  3.08 (  723)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   78 ASP cc_start: 0.8317 (t0) cc_final: 0.8032 (t0)
REVERT: B   60 LYS cc_start: 0.8964 (mttt) cc_final: 0.8724 (mttm)
REVERT: P   73 SER cc_start: 0.8416 (t) cc_final: 0.8052 (t)
  outliers start: 9
  outliers final: 8
  residues processed: 105
  average time/residue: 0.5037
  time to fit residues: 56.4346
Evaluate side-chains
  104 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain O residue   36 VAL
Chi-restraints excluded: chain O residue   87 ARG
Chi-restraints excluded: chain P residue   65 SER
Chi-restraints excluded: chain Q residue   64 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0470
   chunk 73 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   overall best weight:    0.7082

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  69 ASN
A 132 ASN
O 110 ASN
P   8 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.127006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.099109 restraints weight = 10958.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.62
r_work: 0.3121 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8193  Z= 0.143
  Angle     :  0.511   6.913  11447  Z= 0.281
  Chirality :  0.042   0.267   1344
  Planarity :  0.005   0.059   1193
  Dihedral  : 17.969 132.768   2071
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 21.48 %
    Favored  : 77.21 %
  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:  0.10 (0.29), residues: 814
  helix:  1.19 (1.17), residues: 22
  sheet:  0.75 (0.28), residues: 367
  loop : -0.59 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O 133 
 TYR   0.017   0.002   TYR O  60 
 PHE   0.011   0.002   PHE O   6 
 TRP   0.012   0.001   TRP C  90 
 HIS   0.006   0.002   HIS A  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.14 ( 8193)
  covalent geometry    : angle       0.51144 /  0.28 (11447)
  hydrogen bonds       : bond        0.04516 /  2.87 (  302)
  hydrogen bonds       : angle       4.40485 /  3.13 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2660.39 seconds
wall clock time: 46 minutes 0.86 seconds (2760.86 seconds total)