Starting phenix.real_space_refine
on Wed Aug  5 23:46:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10zz_75578/08_2026/10zz_75578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10zz_75578/08_2026/10zz_75578.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/10zz_75578/08_2026/10zz_75578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10zz_75578/08_2026/10zz_75578.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/10zz_75578/08_2026/10zz_75578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10zz_75578/08_2026/10zz_75578.map"
  }
  resolution = 2.8
  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=   0.002 sd=   1.045
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: 6
    Type Number    sf(0)   Gaussians
     P     132      5.49       5
     Mg      2      5.21       5
     S      30      5.16       5
     C    7150      2.51       5
     N    2168      2.21       5
     O    2652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 12134
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "1"
      Number of atoms: 2824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 2824
          Classifications: {'RNA': 132}
          Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 7, 'rna3p_pur': 58, 'rna3p_pyr': 49}
          Link IDs: {'rna2p': 25, 'rna3p': 106}
          Chain breaks: 4
    Chain: "G"
      Number of atoms: 1247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1247
          Classifications: {'peptide': 162}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 153}
    Chain: "N"
      Number of atoms: 1187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1187
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 3507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3507
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 18, 'TRANS': 430}
          Chain breaks: 5
    Chain: "b"
      Number of atoms: 1981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1981
          Classifications: {'peptide': 243}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 229}
          Chain breaks: 2
    Chain: "i"
      Number of atoms: 498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 498
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 1, 'TRANS': 60}
    Chain: "m"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 888
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 3, 'TRANS': 103}
          Chain breaks: 1
    Chain: "1"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.61, per 1000 atoms: 0.22
  Number of scatterers: 12134
  At special positions: 0
  Unit cell: (108.385, 106.26, 132.825, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P     132     15.00
     Mg      2     11.99
     O    2652      8.00
     N    2168      7.00
     C    7150      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: 0.88
  Conformation dependent library (CDL) restraints added in 513.2 milliseconds
  

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 14 sheets defined
      36.4% alpha, 27.6% beta
      38 base pairs and 55 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'G' and resid 72 through 77
    Processing helix  chain 'G' and resid 83 through 96
      removed outlier: 4.050A  pdb=" N   LYS G  96 " --> pdb=" O   LYS G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 101 through 118
    Processing helix  chain 'G' and resid 121 through 126
    Processing helix  chain 'G' and resid 135 through 145
    Processing helix  chain 'G' and resid 159 through 163
    Processing helix  chain 'G' and resid 165 through 174
    Processing helix  chain 'G' and resid 182 through 190
      removed outlier: 3.613A  pdb=" N   LEU G 186 " --> pdb=" O   GLY G 182 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU G 189 " --> pdb=" O   ARG G 185 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL G 190 " --> pdb=" O   LEU G 186 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 204 through 206
      No H-bonds generated for 'chain 'G' and resid 204 through 206'
    Processing helix  chain 'G' and resid 207 through 220
      removed outlier: 3.579A  pdb=" N   ALA G 220 " --> pdb=" O   SER G 216 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 3 through 11
    Processing helix  chain 'N' and resid 16 through 31
    Processing helix  chain 'N' and resid 44 through 51
    Processing helix  chain 'N' and resid 97 through 110
    Processing helix  chain 'N' and resid 139 through 145
      removed outlier: 3.616A  pdb=" N   ASP N 145 " --> pdb=" O   ALA N 141 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 148 through 157
      Proline residue:  N 154  - end of helix
    Processing helix  chain 'R' and resid 80 through 84
    Processing helix  chain 'R' and resid 101 through 106
      removed outlier: 4.197A  pdb=" N   ASN R 106 " --> pdb=" O   PRO R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 131 through 138
    Processing helix  chain 'R' and resid 180 through 183
    Processing helix  chain 'R' and resid 184 through 189
    Processing helix  chain 'R' and resid 485 through 489
    Processing helix  chain 'R' and resid 509 through 516
    Processing helix  chain 'R' and resid 516 through 535
    Processing helix  chain 'R' and resid 539 through 543
    Processing helix  chain 'b' and resid 3 through 9
    Processing helix  chain 'b' and resid 42 through 56
    Processing helix  chain 'b' and resid 72 through 81
      removed outlier: 3.579A  pdb=" N   GLU b  76 " --> pdb=" O   GLN b  72 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 141 through 145
    Processing helix  chain 'b' and resid 146 through 161
    Processing helix  chain 'b' and resid 244 through 271
    Processing helix  chain 'i' and resid 37 through 49
    Processing helix  chain 'i' and resid 51 through 64
    Processing helix  chain 'i' and resid 65 through 78
      removed outlier: 3.665A  pdb=" N   ALA i  69 " --> pdb=" O   GLY i  65 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 79 through 97
    Processing helix  chain 'm' and resid 129 through 135
      removed outlier: 3.518A  pdb=" N   LYS m 135 " --> pdb=" O   LYS m 132 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 197 through 209
    Processing helix  chain 'm' and resid 238 through 263
    Processing helix  chain 'm' and resid 281 through 289
    Processing sheet with id=AA1, first strand: chain 'G' and resid 67 through 70
      removed outlier: 3.527A  pdb=" N   LYS R 111 " --> pdb=" O   SER R 124 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 133 through 134
    Processing sheet with id=AA3, first strand: chain 'N' and resid 36 through 39
      removed outlier: 4.450A  pdb=" N   ILE N  61 " --> pdb=" O   ALA N  39 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   TYR N 127 " --> pdb=" O   GLN N 123 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   GLN N 123 " --> pdb=" O   TYR N 127 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   TYR N 129 " --> pdb=" O   VAL N 121 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   VAL N 135 " --> pdb=" O   VAL N 115 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   VAL N 115 " --> pdb=" O   VAL N 135 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'N' and resid 75 through 76
    Processing sheet with id=AA5, first strand: chain 'R' and resid 2 through 4
      removed outlier: 6.726A  pdb=" N   ALA R 150 " --> pdb=" O   SER R   3 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU R 146 " --> pdb=" O   VAL R   8 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 2 through 4
      removed outlier: 6.726A  pdb=" N   ALA R 150 " --> pdb=" O   SER R   3 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   SER R 157 " --> pdb=" O   MET R 204 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   MET R 204 " --> pdb=" O   SER R 157 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU R 159 " --> pdb=" O   ASP R 202 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ASP R 202 " --> pdb=" O   LEU R 159 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ILE R 161 " --> pdb=" O   HIS R 200 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'R' and resid 209 through 217
      removed outlier: 4.588A  pdb=" N   TYR R 217 " --> pdb=" O   ALA R 227 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   ALA R 227 " --> pdb=" O   TYR R 217 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 289 through 294
      removed outlier: 6.542A  pdb=" N   VAL R 311 " --> pdb=" O   SER R 324 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   SER R 324 " --> pdb=" O   VAL R 311 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU R 313 " --> pdb=" O   ALA R 322 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASN R 320 " --> pdb=" O   ASP R 315 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 334 through 339
      removed outlier: 3.695A  pdb=" N   SER R 336 " --> pdb=" O   GLY R 350 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY R 351 " --> pdb=" O   ARG R 355 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ARG R 355 " --> pdb=" O   GLY R 351 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 381 through 386
      removed outlier: 4.502A  pdb=" N   ASN R 400 " --> pdb=" O   THR R 396 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TRP R 416 " --> pdb=" O   SER R 403 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   PHE m 275 " --> pdb=" O   THR R 417 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 425 through 430
      removed outlier: 4.798A  pdb=" N   ALA R 442 " --> pdb=" O   THR R 447 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   THR R 447 " --> pdb=" O   ALA R 442 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   VAL R 448 " --> pdb=" O   SER R 469 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   SER R 469 " --> pdb=" O   VAL R 448 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU R 450 " --> pdb=" O   VAL R 467 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 477 through 482
    Processing sheet with id=AB4, first strand: chain 'b' and resid 59 through 61
      removed outlier: 6.325A  pdb=" N   LEU b  34 " --> pdb=" O   LEU b  87 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   PHE b  89 " --> pdb=" O   LEU b  34 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ILE b  36 " --> pdb=" O   PHE b  89 " (cutoff:3.500A)
      removed outlier: 8.467A  pdb=" N   ALA b  91 " --> pdb=" O   ILE b  36 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   LEU b  97 " --> pdb=" O   ILE b 114 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   THR b 109 " --> pdb=" O   ILE b 226 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ILE b 226 " --> pdb=" O   THR b 109 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LYS b 111 " --> pdb=" O   ILE b 224 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LEU b 117 " --> pdb=" O   ARG b 218 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ARG b 218 " --> pdb=" O   LEU b 117 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   ILE b 224 " --> pdb=" O   GLU b 238 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   GLU b 238 " --> pdb=" O   ILE b 224 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   ILE b 226 " --> pdb=" O   ILE b 236 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'b' and resid 59 through 61
      removed outlier: 6.325A  pdb=" N   LEU b  34 " --> pdb=" O   LEU b  87 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   PHE b  89 " --> pdb=" O   LEU b  34 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ILE b  36 " --> pdb=" O   PHE b  89 " (cutoff:3.500A)
      removed outlier: 8.467A  pdb=" N   ALA b  91 " --> pdb=" O   ILE b  36 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   LEU b  97 " --> pdb=" O   ILE b 114 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   THR b 109 " --> pdb=" O   ILE b 226 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ILE b 226 " --> pdb=" O   THR b 109 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LYS b 111 " --> pdb=" O   ILE b 224 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LEU b 117 " --> pdb=" O   ARG b 218 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ARG b 218 " --> pdb=" O   LEU b 117 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL b 213 " --> pdb=" O   SER b 194 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   SER b 194 " --> pdb=" O   VAL b 213 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ILE b 215 " --> pdb=" O   GLU b 192 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   GLU b 192 " --> pdb=" O   ILE b 215 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR b 190 " --> pdb=" O   PRO b 217 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   VAL b 136 " --> pdb=" O   MET b 177 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   PHE b 179 " --> pdb=" O   VAL b 136 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   SER b 138 " --> pdb=" O   PHE b 179 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ILE b 181 " --> pdb=" O   SER b 138 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   LEU b 137 " --> pdb=" O   VAL m 223 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      93 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      55 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2246
        1.33 -     1.45: 3662
        1.45 -     1.57: 6428
        1.57 -     1.69: 259
        1.69 -     1.81: 52
  Bond restraints: 12647
  Sorted by residual:
  bond pdb=" N   MET R   1 "
       pdb=" CA  MET R   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.85e+00
  bond pdb=" N9    A 1 268 "
       pdb=" C4    A 1 268 "
    ideal  model  delta    sigma   weight residual
    1.374  1.364  0.010 6.00e-03 2.78e+04 2.83e+00
  bond pdb=" N7    A 1 295 "
       pdb=" C5    A 1 295 "
    ideal  model  delta    sigma   weight residual
    1.388  1.379  0.009 6.00e-03 2.78e+04 2.36e+00
  bond pdb=" C2    U 1 149 "
       pdb=" N3    U 1 149 "
    ideal  model  delta    sigma   weight residual
    1.373  1.363  0.010 7.00e-03 2.04e+04 2.06e+00
  bond pdb=" C6    A 1 123 "
       pdb=" N1    A 1 123 "
    ideal  model  delta    sigma   weight residual
    1.351  1.341  0.010 7.00e-03 2.04e+04 2.02e+00
  ... (remaining 12642 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 16796
        1.37 -     2.74: 805
        2.74 -     4.11: 88
        4.11 -     5.48: 14
        5.48 -     6.85: 5
  Bond angle restraints: 17708
  Sorted by residual:
  angle pdb=" O4'   A 1  65 "
        pdb=" C1'   A 1  65 "
        pdb=" N9    A 1  65 "
      ideal   model   delta    sigma   weight residual
     108.20  112.20   -4.00 8.00e-01 1.56e+00 2.50e+01
  angle pdb=" O5'   A 1 122 "
        pdb=" C5'   A 1 122 "
        pdb=" C4'   A 1 122 "
      ideal   model   delta    sigma   weight residual
     109.40  112.91   -3.51 8.00e-01 1.56e+00 1.92e+01
  angle pdb=" O5'   G 1 143 "
        pdb=" C5'   G 1 143 "
        pdb=" C4'   G 1 143 "
      ideal   model   delta    sigma   weight residual
     109.40  112.80   -3.40 8.00e-01 1.56e+00 1.81e+01
  angle pdb=" O5'   G 1 320 "
        pdb=" C5'   G 1 320 "
        pdb=" C4'   G 1 320 "
      ideal   model   delta    sigma   weight residual
     109.40  112.78   -3.38 8.00e-01 1.56e+00 1.78e+01
  angle pdb=" O5'   C 1  72 "
        pdb=" C5'   C 1  72 "
        pdb=" C4'   C 1  72 "
      ideal   model   delta    sigma   weight residual
     109.40  112.71   -3.31 8.00e-01 1.56e+00 1.71e+01
  ... (remaining 17703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.56: 7054
       20.56 -    41.12: 467
       41.12 -    61.68: 172
       61.68 -    82.24: 99
       82.24 -   102.80: 4
  Dihedral angle restraints: 7796
    sinusoidal: 4387
      harmonic: 3409
  Sorted by residual:
  dihedral pdb=" CA  LYS b 170 "
           pdb=" C   LYS b 170 "
           pdb=" N   PRO b 171 "
           pdb=" CA  PRO b 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.69  -19.31     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  ARG R 542 "
           pdb=" C   ARG R 542 "
           pdb=" N   LYS R 543 "
           pdb=" CA  LYS R 543 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.40  -16.60     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CG  ARG G 108 "
           pdb=" CD  ARG G 108 "
           pdb=" NE  ARG G 108 "
           pdb=" CZ  ARG G 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.40   44.40     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 7793 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1307
       0.034 -    0.068: 448
       0.068 -    0.102: 183
       0.102 -    0.136: 119
       0.136 -    0.170: 11
  Chirality restraints: 2068
  Sorted by residual:
  chirality pdb=" C1'   A 1 323 "
            pdb=" O4'   A 1 323 "
            pdb=" C2'   A 1 323 "
            pdb=" N9    A 1 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.30    0.17 2.00e-01 2.50e+01 7.21e-01
  chirality pdb=" CA  PRO b 171 "
            pdb=" N   PRO b 171 "
            pdb=" C   PRO b 171 "
            pdb=" CB  PRO b 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" C1'   U 1 118 "
            pdb=" O4'   U 1 118 "
            pdb=" C2'   U 1 118 "
            pdb=" N1    U 1 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.33    0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 2065 not shown)

  Planarity restraints: 1779
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 1  65 "   -0.036 2.00e-02 2.50e+03   1.62e-02 7.18e+00
        pdb=" N9    A 1  65 "    0.036 2.00e-02 2.50e+03
        pdb=" C8    A 1  65 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    A 1  65 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A 1  65 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A 1  65 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A 1  65 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    A 1  65 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A 1  65 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A 1  65 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A 1  65 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 1 296 "    0.029 2.00e-02 2.50e+03   1.27e-02 4.45e+00
        pdb=" N9    A 1 296 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8    A 1 296 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A 1 296 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A 1 296 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A 1 296 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A 1 296 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A 1 296 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    A 1 296 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A 1 296 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A 1 296 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 1 323 "   -0.028 2.00e-02 2.50e+03   1.25e-02 4.28e+00
        pdb=" N9    A 1 323 "    0.029 2.00e-02 2.50e+03
        pdb=" C8    A 1 323 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A 1 323 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A 1 323 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A 1 323 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A 1 323 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A 1 323 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A 1 323 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A 1 323 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A 1 323 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1776 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 100
        2.59 -     3.16: 9561
        3.16 -     3.74: 19745
        3.74 -     4.32: 29324
        4.32 -     4.90: 45027
  Nonbonded interactions: 103757
  Sorted by model distance:
  nonbonded pdb=" OP2   A 1 317 "
            pdb="MG    MG 13402 "
     model   vdw
     2.007 2.170
  nonbonded pdb=" OH  TYR G  97 "
            pdb=" OD2 ASP G 207 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O2'   G 1  86 "
            pdb=" O6    G 1  98 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   SER R 108 "
            pdb=" NZ  LYS R 111 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" OG1 THR N  43 "
            pdb=" OE2 GLU N 131 "
     model   vdw
     2.172 3.040
  ... (remaining 103752 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.530
  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:                    0.030
  Process input model:                     12.940
  Find NCS groups from input model:        0.050
  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:7.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
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      :  0.004   0.039  12647  Z= 0.228
  Angle     :  0.640   6.851  17708  Z= 0.460
  Chirality :  0.047   0.170   2068
  Planarity :  0.004   0.059   1779
  Dihedral  : 16.813 102.796   5576
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.88 (0.25), residues: 1131
  helix:  1.28 (0.27), residues: 380
  sheet:  0.41 (0.30), residues: 271
  loop :  0.28 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG b  44 
 TYR   0.015   0.002   TYR b   5 
 PHE   0.018   0.002   PHE i  39 
 TRP   0.009   0.002   TRP R 242 
 HIS   0.005   0.001   HIS m 215 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.23 (12647)
  covalent geometry    : angle       0.64007 /  0.46 (17708)
  hydrogen bonds       : bond        0.11407 / 13.23 (  510)
  hydrogen bonds       : angle       5.14863 /  6.94 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.517 
Fit side-chains
REVERT: m  241 GLU cc_start: 0.7952 (tt0) cc_final: 0.7742 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.7007
  time to fit residues: 152.9917
Evaluate side-chains
  150 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.4980
   chunk 123 optimal weight:    0.1980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.5098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  95 ASN
b 241 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.122946 restraints weight = 13233.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.15
r_work: 0.3228 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12647  Z= 0.115
  Angle     :  0.497   5.324  17708  Z= 0.281
  Chirality :  0.039   0.180   2068
  Planarity :  0.004   0.054   1779
  Dihedral  : 17.707  99.153   3250
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  9.76 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.25), residues: 1131
  helix:  1.64 (0.27), residues: 378
  sheet:  0.59 (0.31), residues: 274
  loop :  0.35 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  68 
 TYR   0.012   0.001   TYR b  43 
 PHE   0.012   0.001   PHE i  39 
 TRP   0.011   0.001   TRP R 416 
 HIS   0.004   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.12 (12647)
  covalent geometry    : angle       0.49668 /  0.28 (17708)
  hydrogen bonds       : bond        0.04783 /  5.12 (  510)
  hydrogen bonds       : angle       4.36901 /  5.98 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.295 
Fit side-chains
REVERT: G   67 ILE cc_start: 0.8290 (tp) cc_final: 0.8021 (pt)
REVERT: G   68 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7637 (tpt-90)
REVERT: G   92 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8204 (ttpt)
REVERT: R  202 ASP cc_start: 0.8098 (p0) cc_final: 0.7863 (p0)
REVERT: R  437 MET cc_start: 0.8983 (ttm) cc_final: 0.8781 (ttm)
REVERT: b  261 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7870 (ttmm)
REVERT: m  259 ASP cc_start: 0.7870 (m-30) cc_final: 0.7637 (m-30)
REVERT: m  260 GLU cc_start: 0.8014 (tp30) cc_final: 0.7375 (tt0)
  outliers start: 16
  outliers final: 9
  residues processed: 175
  average time/residue: 0.6441
  time to fit residues: 120.9843
Evaluate side-chains
  166 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain b residue  261 LYS
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   75 LYS
Chi-restraints excluded: chain m residue  199 LYS
Chi-restraints excluded: chain m residue  240 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 3 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 110 optimal weight:    0.6980
   overall best weight:    1.8384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b 241 GLN
m 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.120127 restraints weight = 13225.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.70
r_work: 0.3062 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12647  Z= 0.225
  Angle     :  0.593   7.187  17708  Z= 0.323
  Chirality :  0.045   0.196   2068
  Planarity :  0.005   0.081   1779
  Dihedral  : 17.683  96.687   3250
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.24 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.25), residues: 1131
  helix:  1.47 (0.26), residues: 378
  sheet:  0.64 (0.30), residues: 287
  loop :  0.23 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 510 
 TYR   0.013   0.002   TYR G  80 
 PHE   0.018   0.002   PHE b 172 
 TRP   0.015   0.002   TRP b 100 
 HIS   0.007   0.002   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00509 /  0.23 (12647)
  covalent geometry    : angle       0.59303 /  0.32 (17708)
  hydrogen bonds       : bond        0.05474 /  5.99 (  510)
  hydrogen bonds       : angle       4.41635 /  6.04 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.410 
Fit side-chains
REVERT: G   68 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.7755 (tpt-90)
REVERT: R  341 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6851 (pmm)
REVERT: m  259 ASP cc_start: 0.7809 (m-30) cc_final: 0.7520 (m-30)
REVERT: m  260 GLU cc_start: 0.8037 (tp30) cc_final: 0.7489 (tt0)
  outliers start: 28
  outliers final: 12
  residues processed: 167
  average time/residue: 0.6152
  time to fit residues: 110.6551
Evaluate side-chains
  161 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  341 MET
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  392 ILE
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain R residue  429 CYS
Chi-restraints excluded: chain R residue  545 THR
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   81 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0970
   chunk 10 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b  82 ASN
b 241 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120447 restraints weight = 13214.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.72
r_work: 0.3069 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12647  Z= 0.199
  Angle     :  0.546   6.086  17708  Z= 0.302
  Chirality :  0.043   0.187   2068
  Planarity :  0.005   0.044   1779
  Dihedral  : 17.686  97.572   3250
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.71 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.25), residues: 1131
  helix:  1.49 (0.26), residues: 380
  sheet:  0.70 (0.30), residues: 287
  loop :  0.13 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG i  82 
 TYR   0.012   0.002   TYR b   5 
 PHE   0.015   0.002   PHE b 172 
 TRP   0.013   0.002   TRP b 100 
 HIS   0.006   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00447 /  0.20 (12647)
  covalent geometry    : angle       0.54585 /  0.30 (17708)
  hydrogen bonds       : bond        0.05200 /  5.59 (  510)
  hydrogen bonds       : angle       4.32971 /  5.91 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.387 
Fit side-chains
REVERT: G   68 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7792 (tpt-90)
REVERT: G   92 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8206 (ttpp)
REVERT: R  182 GLU cc_start: 0.7191 (tp30) cc_final: 0.6861 (pp20)
REVERT: R  189 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7274 (mtp-110)
REVERT: R  225 GLU cc_start: 0.7556 (mp0) cc_final: 0.7323 (mp0)
REVERT: R  341 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6736 (pmm)
REVERT: m  259 ASP cc_start: 0.7869 (m-30) cc_final: 0.7639 (m-30)
REVERT: m  260 GLU cc_start: 0.8071 (tp30) cc_final: 0.7492 (tt0)
  outliers start: 24
  outliers final: 13
  residues processed: 167
  average time/residue: 0.5393
  time to fit residues: 97.3236
Evaluate side-chains
  162 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  341 MET
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  392 ILE
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain R residue  429 CYS
Chi-restraints excluded: chain R residue  545 THR
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   79 SER
Chi-restraints excluded: chain i residue   81 THR
Chi-restraints excluded: chain m residue  240 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0980
   chunk 6 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0060
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0870
   chunk 19 optimal weight:    0.0060
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G 138 HIS
R 409 ASN
b 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.153241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.124800 restraints weight = 13317.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.10
r_work: 0.3256 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  12647  Z= 0.094
  Angle     :  0.446   5.234  17708  Z= 0.256
  Chirality :  0.037   0.159   2068
  Planarity :  0.003   0.028   1779
  Dihedral  : 17.626  99.067   3250
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.89 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.25), residues: 1131
  helix:  1.85 (0.27), residues: 380
  sheet:  0.73 (0.31), residues: 279
  loop :  0.23 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 510 
 TYR   0.014   0.001   TYR i  53 
 PHE   0.008   0.001   PHE b 219 
 TRP   0.013   0.001   TRP R 416 
 HIS   0.003   0.001   HIS b  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00182 /  0.09 (12647)
  covalent geometry    : angle       0.44623 /  0.26 (17708)
  hydrogen bonds       : bond        0.04225 /  4.44 (  510)
  hydrogen bonds       : angle       3.99565 /  5.43 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: G   68 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7691 (tpt-90)
REVERT: G   92 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8143 (ttpp)
REVERT: R  182 GLU cc_start: 0.7134 (tp30) cc_final: 0.6749 (pp20)
REVERT: R  189 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.7201 (mtp-110)
REVERT: R  225 GLU cc_start: 0.7735 (mp0) cc_final: 0.7489 (mp0)
REVERT: R  327 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7872 (m)
REVERT: m  259 ASP cc_start: 0.7813 (m-30) cc_final: 0.7601 (m-30)
REVERT: m  260 GLU cc_start: 0.7994 (tp30) cc_final: 0.7395 (tt0)
  outliers start: 17
  outliers final: 10
  residues processed: 163
  average time/residue: 0.6367
  time to fit residues: 112.0651
Evaluate side-chains
  158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  107 GLU
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  376 MET
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   81 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 61 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 119 optimal weight:    0.0870
   overall best weight:    1.3562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R 522 ASN
b 241 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.149284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.119352 restraints weight = 13162.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.15
r_work: 0.3189 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12647  Z= 0.173
  Angle     :  0.511   5.422  17708  Z= 0.282
  Chirality :  0.041   0.180   2068
  Planarity :  0.004   0.038   1779
  Dihedral  : 17.597  97.806   3250
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.89 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.25), residues: 1131
  helix:  1.75 (0.26), residues: 380
  sheet:  0.86 (0.31), residues: 287
  loop :  0.21 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 510 
 TYR   0.014   0.002   TYR b   5 
 PHE   0.012   0.002   PHE R 453 
 TRP   0.012   0.002   TRP R   7 
 HIS   0.007   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.17 (12647)
  covalent geometry    : angle       0.51089 /  0.28 (17708)
  hydrogen bonds       : bond        0.04780 /  5.19 (  510)
  hydrogen bonds       : angle       4.10715 /  5.59 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.418 
Fit side-chains
REVERT: G   68 ARG cc_start: 0.8336 (tpp-160) cc_final: 0.7766 (tpt-90)
REVERT: R  182 GLU cc_start: 0.7138 (tp30) cc_final: 0.6785 (pp20)
REVERT: R  189 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7211 (mtp-110)
REVERT: R  225 GLU cc_start: 0.7597 (mp0) cc_final: 0.7372 (mp0)
REVERT: R  341 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6792 (pmm)
REVERT: b  183 ASP cc_start: 0.7539 (t0) cc_final: 0.7315 (t0)
REVERT: m  259 ASP cc_start: 0.7869 (m-30) cc_final: 0.7580 (m-30)
REVERT: m  260 GLU cc_start: 0.7963 (tp30) cc_final: 0.7340 (tt0)
  outliers start: 19
  outliers final: 14
  residues processed: 157
  average time/residue: 0.6627
  time to fit residues: 112.2265
Evaluate side-chains
  160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  341 MET
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  376 MET
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  392 ILE
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain R residue  429 CYS
Chi-restraints excluded: chain R residue  545 THR
Chi-restraints excluded: chain b residue  180 SER
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   81 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 114 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0010
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0570
   chunk 84 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.4704

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b 241 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.152352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.124605 restraints weight = 13184.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.07
r_work: 0.3247 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12647  Z= 0.100
  Angle     :  0.444   6.663  17708  Z= 0.250
  Chirality :  0.037   0.158   2068
  Planarity :  0.003   0.031   1779
  Dihedral  : 17.585  98.687   3250
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.38 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.25), residues: 1131
  helix:  1.90 (0.27), residues: 380
  sheet:  0.83 (0.31), residues: 279
  loop :  0.25 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 510 
 TYR   0.014   0.001   TYR b   5 
 PHE   0.009   0.001   PHE b 112 
 TRP   0.012   0.001   TRP R 416 
 HIS   0.003   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00206 /  0.10 (12647)
  covalent geometry    : angle       0.44397 /  0.25 (17708)
  hydrogen bonds       : bond        0.04219 /  4.44 (  510)
  hydrogen bonds       : angle       3.92545 /  5.33 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.418 
Fit side-chains
REVERT: G   68 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7701 (tpt-90)
REVERT: G   92 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8196 (ttpp)
REVERT: R  182 GLU cc_start: 0.7147 (tp30) cc_final: 0.6787 (pp20)
REVERT: R  189 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.7210 (mtp-110)
REVERT: R  225 GLU cc_start: 0.7770 (mp0) cc_final: 0.7566 (mp0)
REVERT: R  327 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7935 (m)
REVERT: R  341 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6843 (pmm)
REVERT: b  183 ASP cc_start: 0.7657 (t0) cc_final: 0.7454 (t0)
REVERT: m  259 ASP cc_start: 0.7815 (m-30) cc_final: 0.7583 (m-30)
REVERT: m  260 GLU cc_start: 0.7903 (tp30) cc_final: 0.7390 (tt0)
  outliers start: 18
  outliers final: 10
  residues processed: 158
  average time/residue: 0.6872
  time to fit residues: 116.7790
Evaluate side-chains
  158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  341 MET
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  376 MET
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain b residue  180 SER
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   81 THR
Chi-restraints excluded: chain m residue  279 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  79 GLN
b  82 ASN
b 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.120025 restraints weight = 13285.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.15
r_work: 0.3211 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12647  Z= 0.134
  Angle     :  0.473   6.935  17708  Z= 0.263
  Chirality :  0.039   0.172   2068
  Planarity :  0.004   0.035   1779
  Dihedral  : 17.565  98.041   3250
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.78 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.25), residues: 1131
  helix:  1.85 (0.26), residues: 380
  sheet:  0.88 (0.31), residues: 288
  loop :  0.28 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 510 
 TYR   0.016   0.001   TYR b   5 
 PHE   0.010   0.001   PHE R 386 
 TRP   0.010   0.001   TRP R 416 
 HIS   0.006   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 (12647)
  covalent geometry    : angle       0.47294 /  0.26 (17708)
  hydrogen bonds       : bond        0.04448 /  4.78 (  510)
  hydrogen bonds       : angle       3.97395 /  5.41 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.382 
Fit side-chains
REVERT: G   68 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.7681 (tpt-90)
REVERT: G   92 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8171 (ttpp)
REVERT: R  182 GLU cc_start: 0.7150 (tp30) cc_final: 0.6768 (pp20)
REVERT: R  189 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.7180 (mtp-110)
REVERT: R  225 GLU cc_start: 0.7735 (mp0) cc_final: 0.7512 (mp0)
REVERT: R  341 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6749 (pmm)
REVERT: b  183 ASP cc_start: 0.7698 (t0) cc_final: 0.7486 (t0)
REVERT: m  259 ASP cc_start: 0.7876 (m-30) cc_final: 0.7573 (m-30)
REVERT: m  260 GLU cc_start: 0.7931 (tp30) cc_final: 0.7381 (tt0)
  outliers start: 17
  outliers final: 13
  residues processed: 159
  average time/residue: 0.6866
  time to fit residues: 117.3438
Evaluate side-chains
  160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  341 MET
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  376 MET
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain R residue  429 CYS
Chi-restraints excluded: chain b residue  180 SER
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   81 THR
Chi-restraints excluded: chain m residue  279 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0040
   chunk 99 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    1.3596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b 241 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.148408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118310 restraints weight = 13124.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.25
r_work: 0.3171 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12647  Z= 0.176
  Angle     :  0.523   6.773  17708  Z= 0.287
  Chirality :  0.041   0.178   2068
  Planarity :  0.004   0.040   1779
  Dihedral  : 17.610  96.981   3250
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.48 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.25), residues: 1131
  helix:  1.70 (0.26), residues: 380
  sheet:  0.85 (0.31), residues: 283
  loop :  0.20 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 510 
 TYR   0.017   0.002   TYR b   5 
 PHE   0.013   0.002   PHE b 172 
 TRP   0.012   0.002   TRP R   7 
 HIS   0.006   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.18 (12647)
  covalent geometry    : angle       0.52290 /  0.29 (17708)
  hydrogen bonds       : bond        0.04843 /  5.22 (  510)
  hydrogen bonds       : angle       4.13016 /  5.61 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.426 
Fit side-chains
REVERT: G   68 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7758 (tpt-90)
REVERT: G   92 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8209 (ttpp)
REVERT: R  182 GLU cc_start: 0.7158 (tp30) cc_final: 0.6778 (pp20)
REVERT: R  189 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7237 (mtp-110)
REVERT: R  225 GLU cc_start: 0.7626 (mp0) cc_final: 0.7396 (mp0)
REVERT: R  341 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6820 (pmm)
REVERT: b  183 ASP cc_start: 0.8080 (t0) cc_final: 0.7858 (t0)
REVERT: m  259 ASP cc_start: 0.7929 (m-30) cc_final: 0.7635 (m-30)
REVERT: m  260 GLU cc_start: 0.8000 (tp30) cc_final: 0.7431 (tt0)
  outliers start: 18
  outliers final: 15
  residues processed: 153
  average time/residue: 0.6533
  time to fit residues: 108.0400
Evaluate side-chains
  157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  145 ASN
Chi-restraints excluded: chain N residue  126 THR
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  341 MET
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  376 MET
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain R residue  429 CYS
Chi-restraints excluded: chain b residue  180 SER
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   58 ILE
Chi-restraints excluded: chain i residue   81 THR
Chi-restraints excluded: chain m residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 93 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9990
   chunk 59 optimal weight:    0.3980
   chunk 68 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 109 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0020
   overall best weight:    0.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b 241 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.150962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.121062 restraints weight = 13338.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.24
r_work: 0.3221 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12647  Z= 0.106
  Angle     :  0.459   8.506  17708  Z= 0.257
  Chirality :  0.038   0.162   2068
  Planarity :  0.004   0.034   1779
  Dihedral  : 17.573  97.738   3250
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 16.07 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.25), residues: 1131
  helix:  1.88 (0.27), residues: 380
  sheet:  0.91 (0.31), residues: 273
  loop :  0.23 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 510 
 TYR   0.016   0.001   TYR b   5 
 PHE   0.011   0.001   PHE b 112 
 TRP   0.015   0.001   TRP R 416 
 HIS   0.004   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00224 /  0.11 (12647)
  covalent geometry    : angle       0.45900 /  0.26 (17708)
  hydrogen bonds       : bond        0.04266 /  4.51 (  510)
  hydrogen bonds       : angle       3.93090 /  5.34 ( 1352)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.415 
Fit side-chains
REVERT: G   68 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.7793 (tpt-90)
REVERT: G   92 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8173 (ttpp)
REVERT: G  207 ASP cc_start: 0.7677 (m-30) cc_final: 0.7458 (m-30)
REVERT: R  182 GLU cc_start: 0.7097 (tp30) cc_final: 0.6752 (pp20)
REVERT: R  189 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.7254 (mtp-110)
REVERT: R  225 GLU cc_start: 0.7786 (mp0) cc_final: 0.7568 (mp0)
REVERT: R  341 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6566 (pmm)
REVERT: m  259 ASP cc_start: 0.7892 (m-30) cc_final: 0.7603 (m-30)
REVERT: m  260 GLU cc_start: 0.7910 (tp30) cc_final: 0.7379 (tt0)
  outliers start: 14
  outliers final: 11
  residues processed: 154
  average time/residue: 0.6686
  time to fit residues: 110.9708
Evaluate side-chains
  158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  145 ASN
Chi-restraints excluded: chain N residue  151 ILE
Chi-restraints excluded: chain R residue  327 SER
Chi-restraints excluded: chain R residue  341 MET
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain R residue  427 THR
Chi-restraints excluded: chain R residue  429 CYS
Chi-restraints excluded: chain b residue  180 SER
Chi-restraints excluded: chain b residue  210 ILE
Chi-restraints excluded: chain i residue   56 ARG
Chi-restraints excluded: chain i residue   81 THR
Chi-restraints excluded: chain m residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0020
   chunk 125 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    1.1792

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N  32 GLN
b 241 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.149214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.121034 restraints weight = 13156.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.06
r_work: 0.3211 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12647  Z= 0.158
  Angle     :  0.510   8.477  17708  Z= 0.281
  Chirality :  0.040   0.176   2068
  Planarity :  0.004   0.039   1779
  Dihedral  : 17.563  96.749   3250
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.27 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.25), residues: 1131
  helix:  1.79 (0.26), residues: 379
  sheet:  0.92 (0.31), residues: 283
  loop :  0.22 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 510 
 TYR   0.022   0.002   TYR b  43 
 PHE   0.012   0.002   PHE b 219 
 TRP   0.011   0.002   TRP R   7 
 HIS   0.007   0.001   HIS b 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 (12647)
  covalent geometry    : angle       0.50967 /  0.28 (17708)
  hydrogen bonds       : bond        0.04635 /  5.02 (  510)
  hydrogen bonds       : angle       4.03140 /  5.49 ( 1352)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4448.08 seconds
wall clock time: 76 minutes 37.82 seconds (4597.82 seconds total)