Starting phenix.real_space_refine
on Thu Jul  2 19:07:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9j_39081/07_2026/8y9j_39081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9j_39081/07_2026/8y9j_39081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y9j_39081/07_2026/8y9j_39081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9j_39081/07_2026/8y9j_39081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9j_39081/07_2026/8y9j_39081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9j_39081/07_2026/8y9j_39081.cif"
  }
  resolution = 4.6
  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=   0.001 sd=   0.022
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      12      5.49       5
     S      41      5.16       5
     C    6190      2.51       5
     N    1704      2.21       5
     O    1823      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9770
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3071
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 8, 'TRANS': 381}
    Chain: "B"
      Number of atoms: 3066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3066
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 8, 'TRANS': 380}
    Chain: "C"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1764
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 9, 'TRANS': 212}
    Chain: "D"
      Number of atoms: 1629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1629
          Classifications: {'peptide': 204}
          Link IDs: {'PTRANS': 8, 'TRANS': 195}
    Chain: "K"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 240
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
  Time building chain proxies: 1.77, per 1000 atoms: 0.18
  Number of scatterers: 9770
  At special positions: 0
  Unit cell: (116.325, 120.037, 106.425, 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      41     16.00
     P      12     15.00
     O    1823      8.00
     N    1704      7.00
     C    6190      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: 0.82
  Conformation dependent library (CDL) restraints added in 316.1 milliseconds
  

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      69.2% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 29
    Processing helix  chain 'A' and resid 48 through 64
      removed outlier: 3.952A  pdb=" N   ILE A  52 " --> pdb=" O   ASN A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 84
      removed outlier: 3.808A  pdb=" N   GLN A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 91
      removed outlier: 4.239A  pdb=" N   LEU A  89 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 124 through 137
      removed outlier: 4.138A  pdb=" N   ASN A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ILE A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 157
      removed outlier: 3.852A  pdb=" N   PHE A 157 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 183
      removed outlier: 4.021A  pdb=" N   LEU A 169 " --> pdb=" O   GLU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 221
      removed outlier: 4.249A  pdb=" N   GLN A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   HIS A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   MET A 198 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG A 202 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG A 205 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   THR A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   LEU A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ILE A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
      removed outlier: 3.821A  pdb=" N   ALA A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 290
      removed outlier: 3.714A  pdb=" N   GLU A 276 " --> pdb=" O   LYS A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.648A  pdb=" N   ARG A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU A 299 " --> pdb=" O   PRO A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 308
      removed outlier: 3.665A  pdb=" N   ASN A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 329
    Processing helix  chain 'A' and resid 330 through 335
      removed outlier: 3.594A  pdb=" N   GLY A 333 " --> pdb=" O   THR A 330 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ASN A 335 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 366
      removed outlier: 3.523A  pdb=" N   LEU A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASP A 364 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 408
    Processing helix  chain 'B' and resid 21 through 28
      removed outlier: 4.120A  pdb=" N   LEU B  25 " --> pdb=" O   TYR B  21 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY B  28 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 64
      removed outlier: 3.827A  pdb=" N   VAL B  64 " --> pdb=" O   PHE B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 83
    Processing helix  chain 'B' and resid 85 through 93
      removed outlier: 4.215A  pdb=" N   LEU B  89 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 115 through 121
    Processing helix  chain 'B' and resid 124 through 137
      removed outlier: 3.790A  pdb=" N   ASN B 129 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG B 132 " --> pdb=" O   LYS B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 157
      removed outlier: 4.017A  pdb=" N   PHE B 157 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 183
      removed outlier: 5.012A  pdb=" N   LYS B 166 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B 169 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 221
      removed outlier: 3.610A  pdb=" N   ARG B 202 " --> pdb=" O   MET B 198 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG B 205 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE B 208 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   LEU B 209 " --> pdb=" O   ARG B 205 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 240
    Processing helix  chain 'B' and resid 244 through 253
    Processing helix  chain 'B' and resid 270 through 291
      removed outlier: 3.875A  pdb=" N   LYS B 289 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   HIS B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
      Proline residue:  B 295  - end of helix
      No H-bonds generated for 'chain 'B' and resid 292 through 297'
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.933A  pdb=" N   ASN B 307 " --> pdb=" O   GLY B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 329
      removed outlier: 3.624A  pdb=" N   HIS B 327 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 335
      removed outlier: 3.587A  pdb=" N   ASN B 335 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 367
      removed outlier: 4.720A  pdb=" N   LEU B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLY B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 407
      removed outlier: 3.756A  pdb=" N   GLU B 372 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 27
      removed outlier: 3.545A  pdb=" N   GLY C  20 " --> pdb=" O   ASP C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 62
      removed outlier: 3.873A  pdb=" N   ALA C  55 " --> pdb=" O   HIS C  51 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU C  56 " --> pdb=" O   LYS C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 76
      removed outlier: 3.693A  pdb=" N   THR C  72 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 81
    Processing helix  chain 'C' and resid 88 through 105
    Processing helix  chain 'C' and resid 115 through 130
      removed outlier: 4.454A  pdb=" N   LEU C 119 " --> pdb=" O   LEU C 115 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR C 128 " --> pdb=" O   ASP C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 144
      removed outlier: 3.900A  pdb=" N   GLN C 144 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 166
      removed outlier: 3.567A  pdb=" N   SER C 151 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 210
      removed outlier: 3.832A  pdb=" N   SER C 207 " --> pdb=" O   PRO C 204 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA C 208 " --> pdb=" O   ASP C 205 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASN C 210 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 230
      removed outlier: 3.758A  pdb=" N   LYS C 228 " --> pdb=" O   GLU C 224 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   PHE C 230 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 61
      removed outlier: 3.763A  pdb=" N   LYS D  61 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 82
      removed outlier: 3.798A  pdb=" N   ASN D  74 " --> pdb=" O   SER D  70 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU D  75 " --> pdb=" O   MET D  71 " (cutoff:3.500A)
      Proline residue:  D  77  - end of helix
    Processing helix  chain 'D' and resid 90 through 106
    Processing helix  chain 'D' and resid 114 through 128
      removed outlier: 3.852A  pdb=" N   ALA D 118 " --> pdb=" O   PRO D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 144
    Processing helix  chain 'D' and resid 145 through 166
      removed outlier: 4.085A  pdb=" N   MET D 149 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA D 166 " --> pdb=" O   ASN D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 211
    Processing helix  chain 'D' and resid 223 through 230
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44
      removed outlier: 5.937A  pdb=" N   ARG A  39 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   GLU A 107 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE A  41 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   LYS A 109 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL A  43 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257
    Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 45
      removed outlier: 6.435A  pdb=" N   ARG B  39 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   GLU B 107 " --> pdb=" O   ARG B  39 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ILE B  41 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   LYS B 109 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   VAL B  43 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 258
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 34
    Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 87
      removed outlier: 6.882A  pdb=" N   THR C  86 " --> pdb=" O   PHE C 219 " (cutoff:3.500A)
      removed outlier: 8.794A  pdb=" N   LEU C 221 " --> pdb=" O   THR C  86 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE C 179 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 33
    Processing sheet with id=AA8, first strand: chain 'D' and resid 178 through 182

    595 hydrogen bonds defined for protein.
    1728 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 1.08 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: 2341
        1.33 -     1.45: 2064
        1.45 -     1.58: 5467
        1.58 -     1.70: 23
        1.70 -     1.82: 75
  Bond restraints: 9970
  Sorted by residual:
  bond pdb=" N   PRO D  77 "
       pdb=" CD  PRO D  77 "
    ideal  model  delta    sigma   weight residual
    1.473  1.419  0.054 1.40e-02 5.10e+03 1.51e+01
  bond pdb=" N   THR B 206 "
       pdb=" CA  THR B 206 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.25e-02 6.40e+03 1.14e+01
  bond pdb=" CA  GLN A  84 "
       pdb=" C   GLN A  84 "
    ideal  model  delta    sigma   weight residual
    1.524  1.568 -0.044 1.32e-02 5.74e+03 1.11e+01
  bond pdb=" C4'   U K   9 "
       pdb=" O4'   U K   9 "
    ideal  model  delta    sigma   weight residual
    1.454  1.406  0.048 1.50e-02 4.44e+03 1.04e+01
  bond pdb=" N   GLY D 215 "
       pdb=" CA  GLY D 215 "
    ideal  model  delta    sigma   weight residual
    1.434  1.472 -0.038 1.22e-02 6.72e+03 9.73e+00
  ... (remaining 9965 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 11004
        2.57 -     5.13: 2273
        5.13 -     7.70: 191
        7.70 -    10.27: 36
       10.27 -    12.83: 10
  Bond angle restraints: 13514
  Sorted by residual:
  angle pdb=" N   VAL A 124 "
        pdb=" CA  VAL A 124 "
        pdb=" C   VAL A 124 "
      ideal   model   delta    sigma   weight residual
     110.53  120.75  -10.22 9.40e-01 1.13e+00 1.18e+02
  angle pdb=" C   HIS B 290 "
        pdb=" N   GLY B 291 "
        pdb=" CA  GLY B 291 "
      ideal   model   delta    sigma   weight residual
     120.13  132.96  -12.83 1.26e+00 6.30e-01 1.04e+02
  angle pdb=" CA  PHE B  66 "
        pdb=" CB  PHE B  66 "
        pdb=" CG  PHE B  66 "
      ideal   model   delta    sigma   weight residual
     113.80  123.70   -9.90 1.00e+00 1.00e+00 9.81e+01
  angle pdb=" CA  PHE D 134 "
        pdb=" CB  PHE D 134 "
        pdb=" CG  PHE D 134 "
      ideal   model   delta    sigma   weight residual
     113.80  122.88   -9.08 1.00e+00 1.00e+00 8.25e+01
  angle pdb=" CA  PRO D 114 "
        pdb=" N   PRO D 114 "
        pdb=" CD  PRO D 114 "
      ideal   model   delta    sigma   weight residual
     112.00   99.38   12.62 1.40e+00 5.10e-01 8.13e+01
  ... (remaining 13509 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.88: 5839
       32.88 -    65.76: 198
       65.76 -    98.64: 18
       98.64 -   131.51: 0
      131.51 -   164.39: 2
  Dihedral angle restraints: 6057
    sinusoidal: 2566
      harmonic: 3491
  Sorted by residual:
  dihedral pdb=" C5'   U K  15 "
           pdb=" C4'   U K  15 "
           pdb=" C3'   U K  15 "
           pdb=" O3'   U K  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   67.57   79.43     1      8.00e+00 1.56e-02 1.22e+02
  dihedral pdb=" O4'   U K  15 "
           pdb=" C4'   U K  15 "
           pdb=" C3'   U K  15 "
           pdb=" C2'   U K  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -38.37   62.37     1      8.00e+00 1.56e-02 8.04e+01
  dihedral pdb=" C3'   U K  15 "
           pdb=" C4'   U K  15 "
           pdb=" O4'   U K  15 "
           pdb=" C1'   U K  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   49.77  -51.77     1      8.00e+00 1.56e-02 5.72e+01
  ... (remaining 6054 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.156: 1315
       0.156 -    0.311: 214
       0.311 -    0.467: 27
       0.467 -    0.622: 4
       0.622 -    0.778: 3
  Chirality restraints: 1563
  Sorted by residual:
  chirality pdb=" CA  ASN A 301 "
            pdb=" N   ASN A 301 "
            pdb=" C   ASN A 301 "
            pdb=" CB  ASN A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.73    0.78 2.00e-01 2.50e+01 1.51e+01
  chirality pdb=" CA  ASN A 306 "
            pdb=" N   ASN A 306 "
            pdb=" C   ASN A 306 "
            pdb=" CB  ASN A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.82    0.69 2.00e-01 2.50e+01 1.20e+01
  chirality pdb=" CA  ILE B 254 "
            pdb=" N   ILE B 254 "
            pdb=" C   ILE B 254 "
            pdb=" CB  ILE B 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.79    0.65 2.00e-01 2.50e+01 1.04e+01
  ... (remaining 1560 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U K  16 "    0.376 2.00e-02 2.50e+03   1.74e-01 6.80e+02
        pdb=" N1    U K  16 "   -0.109 2.00e-02 2.50e+03
        pdb=" C2    U K  16 "   -0.119 2.00e-02 2.50e+03
        pdb=" O2    U K  16 "   -0.107 2.00e-02 2.50e+03
        pdb=" N3    U K  16 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    U K  16 "    0.054 2.00e-02 2.50e+03
        pdb=" O4    U K  16 "    0.203 2.00e-02 2.50e+03
        pdb=" C5    U K  16 "   -0.106 2.00e-02 2.50e+03
        pdb=" C6    U K  16 "   -0.193 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U K  11 "   -0.246 2.00e-02 2.50e+03   1.23e-01 3.43e+02
        pdb=" N1    U K  11 "    0.039 2.00e-02 2.50e+03
        pdb=" C2    U K  11 "    0.008 2.00e-02 2.50e+03
        pdb=" O2    U K  11 "    0.152 2.00e-02 2.50e+03
        pdb=" N3    U K  11 "   -0.039 2.00e-02 2.50e+03
        pdb=" C4    U K  11 "   -0.028 2.00e-02 2.50e+03
        pdb=" O4    U K  11 "   -0.135 2.00e-02 2.50e+03
        pdb=" C5    U K  11 "    0.109 2.00e-02 2.50e+03
        pdb=" C6    U K  11 "    0.140 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U K  15 "    0.207 2.00e-02 2.50e+03   1.20e-01 3.27e+02
        pdb=" N1    U K  15 "    0.020 2.00e-02 2.50e+03
        pdb=" C2    U K  15 "    0.009 2.00e-02 2.50e+03
        pdb=" O2    U K  15 "   -0.183 2.00e-02 2.50e+03
        pdb=" N3    U K  15 "    0.068 2.00e-02 2.50e+03
        pdb=" C4    U K  15 "    0.023 2.00e-02 2.50e+03
        pdb=" O4    U K  15 "    0.119 2.00e-02 2.50e+03
        pdb=" C5    U K  15 "   -0.132 2.00e-02 2.50e+03
        pdb=" C6    U K  15 "   -0.130 2.00e-02 2.50e+03
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 3262
        2.88 -     3.39: 11057
        3.39 -     3.89: 16423
        3.89 -     4.40: 18673
        4.40 -     4.90: 29426
  Nonbonded interactions: 78841
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 403 "
            pdb=" OG1 THR A 406 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   ALA B 403 "
            pdb=" OG1 THR B 406 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" O   ILE A 215 "
            pdb=" N   GLY A 218 "
     model   vdw
     2.503 3.120
  nonbonded pdb=" O3'   U K   9 "
            pdb=" O2'   U K   9 "
     model   vdw
     2.511 2.432
  nonbonded pdb=" O2'   U K  15 "
            pdb=" OP1   U K  16 "
     model   vdw
     2.561 3.040
  ... (remaining 78836 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 19 through 407)
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 28 through 231)
  selection = chain 'D'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.300
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
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      :  0.012   0.054   9970  Z= 0.773
  Angle     :  2.024  12.832  13514  Z= 1.417
  Chirality :  0.122   0.778   1563
  Planarity :  0.021   0.391   1689
  Dihedral  : 16.841 164.392   3789
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  2.01 %
    Allowed  :  7.35 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  7.47 %
    Favored  : 90.30 %
  Cbeta Deviations :  1.68 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.20), residues: 1197
  helix: -1.13 (0.16), residues: 663
  sheet:  0.89 (0.50), residues: 88
  loop : -2.94 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 361 
 TYR   0.208   0.032   TYR B 340 
 PHE   0.162   0.021   PHE D 134 
 TRP   0.142   0.026   TRP C  42 
 HIS   0.016   0.004   HIS D  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01226 /  0.77 ( 9970)
  covalent geometry    : angle       2.02369 /  1.42 (13514)
  hydrogen bonds       : bond        0.18979 / 13.04 (  595)
  hydrogen bonds       : angle       8.88888 /  6.48 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 443
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.9007 (mt) cc_final: 0.8480 (mt)
REVERT: A   98 TYR cc_start: 0.7481 (t80) cc_final: 0.7258 (t80)
REVERT: A  105 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8582 (ttt-90)
REVERT: A  107 GLU cc_start: 0.8975 (pt0) cc_final: 0.8736 (pt0)
REVERT: A  110 LYS cc_start: 0.9692 (tptm) cc_final: 0.9303 (tppp)
REVERT: A  128 LYS cc_start: 0.8983 (pttt) cc_final: 0.8778 (pttm)
REVERT: A  174 ARG cc_start: 0.9297 (mtt180) cc_final: 0.9089 (mtp85)
REVERT: A  179 HIS cc_start: 0.8726 (m-70) cc_final: 0.8505 (m-70)
REVERT: A  199 VAL cc_start: 0.9194 (t) cc_final: 0.8957 (m)
REVERT: A  204 MET cc_start: 0.8595 (mmt) cc_final: 0.8015 (tpp)
REVERT: A  211 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8179 (mtmt)
REVERT: A  253 HIS cc_start: 0.8442 (m90) cc_final: 0.8154 (m90)
REVERT: A  280 PHE cc_start: 0.9574 (t80) cc_final: 0.8796 (t80)
REVERT: A  327 HIS cc_start: 0.7234 (m170) cc_final: 0.6576 (m-70)
REVERT: A  342 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.9046 (mp10)
REVERT: A  371 GLN cc_start: 0.9504 (mm-40) cc_final: 0.9263 (mp10)
REVERT: A  372 GLU cc_start: 0.9503 (mp0) cc_final: 0.9236 (mp0)
REVERT: A  376 LEU cc_start: 0.9803 (mm) cc_final: 0.9475 (mm)
REVERT: A  380 HIS cc_start: 0.9494 (m-70) cc_final: 0.9173 (m-70)
REVERT: A  398 ARG cc_start: 0.9073 (ptt90) cc_final: 0.8774 (ttp-110)
REVERT: B   19 MET cc_start: 0.6513 (pmm) cc_final: 0.5581 (pmm)
REVERT: B  157 PHE cc_start: 0.9471 (m-80) cc_final: 0.9123 (m-80)
REVERT: B  194 VAL cc_start: 0.8833 (t) cc_final: 0.8555 (t)
REVERT: B  196 HIS cc_start: 0.9203 (m-70) cc_final: 0.8584 (m-70)
REVERT: B  198 MET cc_start: 0.8960 (mmm) cc_final: 0.8443 (mmm)
REVERT: B  221 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7869 (ppp)
REVERT: B  222 VAL cc_start: 0.5646 (OUTLIER) cc_final: 0.5103 (t)
REVERT: B  234 ASN cc_start: 0.9370 (t0) cc_final: 0.9151 (t0)
REVERT: B  327 HIS cc_start: 0.8087 (m-70) cc_final: 0.7871 (m90)
REVERT: B  330 THR cc_start: 0.9374 (p) cc_final: 0.9036 (t)
REVERT: B  344 ARG cc_start: 0.9031 (ttt-90) cc_final: 0.8636 (tpt-90)
REVERT: B  354 LEU cc_start: 0.9646 (mt) cc_final: 0.9432 (mm)
REVERT: B  355 GLN cc_start: 0.9212 (mt0) cc_final: 0.8649 (mp10)
REVERT: B  363 LEU cc_start: 0.9389 (mt) cc_final: 0.9105 (mt)
REVERT: B  374 LYS cc_start: 0.9309 (mtmm) cc_final: 0.8964 (mttp)
REVERT: B  376 LEU cc_start: 0.9718 (mt) cc_final: 0.9465 (mt)
REVERT: B  380 HIS cc_start: 0.9442 (m90) cc_final: 0.9007 (m90)
REVERT: B  384 ASN cc_start: 0.9073 (m-40) cc_final: 0.8857 (m110)
REVERT: C   52 LYS cc_start: 0.6452 (mttm) cc_final: 0.6106 (mmmt)
REVERT: C   80 PHE cc_start: 0.8714 (t80) cc_final: 0.8489 (t80)
REVERT: C  136 MET cc_start: -0.3641 (tmm) cc_final: -0.4004 (mmm)
REVERT: C  159 LYS cc_start: 0.8174 (mttt) cc_final: 0.7837 (tptp)
REVERT: C  160 PHE cc_start: 0.8835 (t80) cc_final: 0.8338 (t80)
REVERT: C  186 HIS cc_start: 0.8755 (m90) cc_final: 0.8477 (m170)
REVERT: C  191 THR cc_start: 0.8918 (m) cc_final: 0.8693 (p)
REVERT: C  195 MET cc_start: 0.0881 (ttm) cc_final: 0.0548 (ttp)
REVERT: C  200 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7762 (mt-10)
REVERT: C  213 LYS cc_start: 0.8815 (tttt) cc_final: 0.8479 (tmtt)
REVERT: C  230 PHE cc_start: 0.6001 (t80) cc_final: 0.5792 (t80)
REVERT: D   30 LEU cc_start: 0.8749 (mt) cc_final: 0.8142 (mt)
REVERT: D   92 TRP cc_start: 0.8405 (p-90) cc_final: 0.8051 (p-90)
REVERT: D  121 LEU cc_start: 0.9313 (mt) cc_final: 0.8978 (mt)
REVERT: D  124 ASP cc_start: 0.9678 (m-30) cc_final: 0.9473 (p0)
REVERT: D  157 ILE cc_start: 0.9257 (mt) cc_final: 0.8975 (mt)
REVERT: D  165 ASP cc_start: 0.9229 (m-30) cc_final: 0.8932 (m-30)
REVERT: D  209 MET cc_start: 0.2058 (ppp) cc_final: 0.0304 (mmm)
  outliers start: 23
  outliers final: 9
  residues processed: 458
  average time/residue: 0.0797
  time to fit residues: 50.5273
Evaluate side-chains
  338 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 326
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  32 GLN
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 HIS
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 ASN
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 GLN
B 175 GLN
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
B 228 ASN
B 306 ASN
** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 162 ASN
** C 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS
D 202 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.121978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.097260 restraints weight = 31800.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.100436 restraints weight = 21511.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.102856 restraints weight = 15922.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.104656 restraints weight = 12445.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.106024 restraints weight = 10182.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   9970  Z= 0.246
  Angle     :  0.990  13.712  13514  Z= 0.540
  Chirality :  0.051   0.258   1563
  Planarity :  0.008   0.167   1689
  Dihedral  : 13.181 139.498   1464
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  9.44 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  4.46 %
    Favored  : 95.05 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.94 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.22), residues: 1197
  helix: -0.25 (0.18), residues: 678
  sheet:  0.72 (0.46), residues: 107
  loop : -2.77 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 298 
 TYR   0.043   0.004   TYR A  44 
 PHE   0.035   0.003   PHE A 296 
 TRP   0.031   0.003   TRP C  92 
 HIS   0.010   0.002   HIS A 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.25 ( 9970)
  covalent geometry    : angle       0.98998 /  0.54 (13514)
  hydrogen bonds       : bond        0.07708 /  5.35 (  595)
  hydrogen bonds       : angle       6.92425 /  5.07 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 361
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.8978 (tmm) cc_final: 0.8549 (tmm)
REVERT: A   77 LEU cc_start: 0.9202 (mt) cc_final: 0.8581 (mt)
REVERT: A   98 TYR cc_start: 0.7540 (t80) cc_final: 0.7306 (t80)
REVERT: A  110 LYS cc_start: 0.9331 (tptm) cc_final: 0.8939 (tppp)
REVERT: A  153 PHE cc_start: 0.9157 (t80) cc_final: 0.8664 (t80)
REVERT: A  174 ARG cc_start: 0.9340 (mtt180) cc_final: 0.9114 (mtp180)
REVERT: A  179 HIS cc_start: 0.8553 (m-70) cc_final: 0.8171 (m-70)
REVERT: A  204 MET cc_start: 0.8313 (tpp) cc_final: 0.7641 (tpp)
REVERT: A  211 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8764 (mtmt)
REVERT: A  213 LEU cc_start: 0.9488 (tt) cc_final: 0.9150 (tt)
REVERT: A  286 SER cc_start: 0.9103 (t) cc_final: 0.8902 (t)
REVERT: A  359 GLU cc_start: 0.9152 (tt0) cc_final: 0.8657 (tm-30)
REVERT: A  362 GLU cc_start: 0.9536 (OUTLIER) cc_final: 0.9310 (pp20)
REVERT: A  372 GLU cc_start: 0.9481 (mp0) cc_final: 0.9173 (mp0)
REVERT: A  376 LEU cc_start: 0.9745 (mm) cc_final: 0.9284 (mm)
REVERT: A  380 HIS cc_start: 0.9397 (m-70) cc_final: 0.8581 (m90)
REVERT: B   19 MET cc_start: 0.7804 (pmm) cc_final: 0.7092 (pmm)
REVERT: B   76 MET cc_start: 0.9376 (ptp) cc_final: 0.9020 (ptt)
REVERT: B   78 CYS cc_start: 0.8594 (p) cc_final: 0.8352 (p)
REVERT: B  109 LYS cc_start: 0.8897 (mttt) cc_final: 0.8695 (mtpt)
REVERT: B  162 VAL cc_start: 0.8841 (t) cc_final: 0.8569 (t)
REVERT: B  179 HIS cc_start: 0.8726 (m-70) cc_final: 0.8442 (m-70)
REVERT: B  284 LEU cc_start: 0.9594 (mm) cc_final: 0.9100 (pp)
REVERT: B  363 LEU cc_start: 0.9311 (mt) cc_final: 0.9102 (mt)
REVERT: B  376 LEU cc_start: 0.9712 (mt) cc_final: 0.9312 (mt)
REVERT: B  380 HIS cc_start: 0.9308 (m90) cc_final: 0.8758 (m90)
REVERT: C  159 LYS cc_start: 0.8256 (mttt) cc_final: 0.7868 (tptp)
REVERT: C  160 PHE cc_start: 0.8896 (t80) cc_final: 0.8595 (t80)
REVERT: C  181 ILE cc_start: 0.8524 (mm) cc_final: 0.7662 (mp)
REVERT: C  191 THR cc_start: 0.9291 (m) cc_final: 0.9078 (p)
REVERT: C  198 LEU cc_start: 0.9201 (tp) cc_final: 0.8956 (tp)
REVERT: C  200 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8770 (mt-10)
REVERT: C  213 LYS cc_start: 0.8902 (tttt) cc_final: 0.8529 (tmtt)
REVERT: C  222 LEU cc_start: 0.9435 (pp) cc_final: 0.9147 (tp)
REVERT: D   35 ILE cc_start: 0.8929 (tp) cc_final: 0.8676 (tp)
REVERT: D  109 GLN cc_start: 0.8770 (mt0) cc_final: 0.8430 (tt0)
REVERT: D  115 LEU cc_start: 0.9364 (mt) cc_final: 0.8705 (tt)
REVERT: D  119 LEU cc_start: 0.9685 (mt) cc_final: 0.9452 (mt)
REVERT: D  121 LEU cc_start: 0.9186 (mt) cc_final: 0.8867 (mt)
REVERT: D  124 ASP cc_start: 0.9575 (m-30) cc_final: 0.9058 (p0)
REVERT: D  149 MET cc_start: 0.9410 (mpp) cc_final: 0.9085 (mpp)
  outliers start: 5
  outliers final: 0
  residues processed: 363
  average time/residue: 0.0795
  time to fit residues: 39.9175
Evaluate side-chains
  307 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 306
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0870
   chunk 32 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.8164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 192 GLN
A 220 HIS
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.126613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.101604 restraints weight = 31554.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.104955 restraints weight = 21461.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.107476 restraints weight = 15801.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.109422 restraints weight = 12299.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.110877 restraints weight = 9987.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   9970  Z= 0.194
  Angle     :  0.878  15.829  13514  Z= 0.477
  Chirality :  0.048   0.241   1563
  Planarity :  0.007   0.161   1689
  Dihedral  : 12.099 135.492   1464
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.36 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.75 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.51 %

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: -1.21 (0.23), residues: 1197
  helix:  0.02 (0.19), residues: 682
  sheet:  0.75 (0.46), residues: 109
  loop : -2.66 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 192 
 TYR   0.020   0.003   TYR B  98 
 PHE   0.042   0.003   PHE B  66 
 TRP   0.020   0.002   TRP D  69 
 HIS   0.033   0.002   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 ( 9970)
  covalent geometry    : angle       0.87847 /  0.48 (13514)
  hydrogen bonds       : bond        0.06700 /  4.65 (  595)
  hydrogen bonds       : angle       6.53189 /  4.75 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 353
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.8392 (pmm) cc_final: 0.8136 (pmm)
REVERT: A   57 ILE cc_start: 0.9347 (mm) cc_final: 0.8929 (tp)
REVERT: A   76 MET cc_start: 0.9032 (tmm) cc_final: 0.8551 (tmm)
REVERT: A   77 LEU cc_start: 0.9189 (mt) cc_final: 0.8424 (mt)
REVERT: A   79 LEU cc_start: 0.9093 (mm) cc_final: 0.8782 (mm)
REVERT: A  116 ARG cc_start: 0.8252 (mmt-90) cc_final: 0.7690 (mmp80)
REVERT: A  132 ARG cc_start: 0.8754 (mtm110) cc_final: 0.8300 (mtm180)
REVERT: A  179 HIS cc_start: 0.8543 (m-70) cc_final: 0.8102 (m-70)
REVERT: A  232 ILE cc_start: 0.9253 (tt) cc_final: 0.8953 (tt)
REVERT: A  348 THR cc_start: 0.9308 (m) cc_final: 0.9056 (m)
REVERT: A  359 GLU cc_start: 0.9188 (tt0) cc_final: 0.8914 (tt0)
REVERT: A  376 LEU cc_start: 0.9681 (mm) cc_final: 0.9305 (mm)
REVERT: A  377 MET cc_start: 0.9153 (tmm) cc_final: 0.8739 (tmm)
REVERT: A  379 PHE cc_start: 0.9468 (t80) cc_final: 0.9197 (t80)
REVERT: A  380 HIS cc_start: 0.9278 (m-70) cc_final: 0.8645 (m-70)
REVERT: B   21 TYR cc_start: 0.7502 (m-80) cc_final: 0.7013 (m-80)
REVERT: B   76 MET cc_start: 0.9300 (ptp) cc_final: 0.9042 (ptt)
REVERT: B   78 CYS cc_start: 0.8602 (p) cc_final: 0.8380 (p)
REVERT: B  196 HIS cc_start: 0.8394 (m-70) cc_final: 0.8053 (m-70)
REVERT: B  251 LEU cc_start: 0.9266 (pp) cc_final: 0.9018 (mm)
REVERT: B  284 LEU cc_start: 0.9510 (mm) cc_final: 0.9055 (pp)
REVERT: B  338 GLU cc_start: 0.8127 (pm20) cc_final: 0.7750 (pm20)
REVERT: B  363 LEU cc_start: 0.9341 (mt) cc_final: 0.9068 (mt)
REVERT: B  376 LEU cc_start: 0.9676 (mt) cc_final: 0.9276 (mt)
REVERT: B  377 MET cc_start: 0.9455 (ttm) cc_final: 0.8920 (tmm)
REVERT: C   76 PHE cc_start: 0.9030 (m-80) cc_final: 0.8769 (m-80)
REVERT: C  159 LYS cc_start: 0.8083 (mttt) cc_final: 0.7741 (tptp)
REVERT: C  160 PHE cc_start: 0.8765 (t80) cc_final: 0.8486 (t80)
REVERT: C  191 THR cc_start: 0.9125 (m) cc_final: 0.8540 (p)
REVERT: C  198 LEU cc_start: 0.9213 (tp) cc_final: 0.8922 (tp)
REVERT: C  200 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8229 (mt-10)
REVERT: C  213 LYS cc_start: 0.8867 (tttt) cc_final: 0.8484 (tmtt)
REVERT: C  222 LEU cc_start: 0.9379 (pp) cc_final: 0.9114 (tt)
REVERT: D  115 LEU cc_start: 0.9322 (mt) cc_final: 0.8749 (tt)
REVERT: D  119 LEU cc_start: 0.9667 (mt) cc_final: 0.9466 (mt)
REVERT: D  121 LEU cc_start: 0.9082 (mt) cc_final: 0.8632 (mt)
REVERT: D  124 ASP cc_start: 0.9564 (m-30) cc_final: 0.8945 (p0)
REVERT: D  126 LEU cc_start: 0.9772 (mt) cc_final: 0.9571 (mt)
REVERT: D  149 MET cc_start: 0.9322 (mpp) cc_final: 0.8760 (mpp)
REVERT: D  165 ASP cc_start: 0.9230 (m-30) cc_final: 0.8952 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 353
  average time/residue: 0.0759
  time to fit residues: 37.2396
Evaluate side-chains
  316 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 35 optimal weight:    0.6980
   chunk 74 optimal weight:    8.9990
   chunk 81 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 196 HIS
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 GLN
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 ASN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 381 GLN
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 103 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 GLN
D 186 HIS
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.121968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.097481 restraints weight = 32981.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.100837 restraints weight = 22240.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.103311 restraints weight = 16277.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.105216 restraints weight = 12639.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.106655 restraints weight = 10226.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.5553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   9970  Z= 0.220
  Angle     :  0.851  11.942  13514  Z= 0.461
  Chirality :  0.047   0.243   1563
  Planarity :  0.007   0.159   1689
  Dihedral  : 11.598 129.847   1464
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 19.53
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.11 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.27 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.60 %

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: -1.21 (0.23), residues: 1197
  helix: -0.05 (0.19), residues: 678
  sheet:  0.84 (0.46), residues: 112
  loop : -2.55 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 398 
 TYR   0.026   0.002   TYR B  98 
 PHE   0.028   0.003   PHE A 296 
 TRP   0.050   0.003   TRP D  92 
 HIS   0.020   0.002   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.22 ( 9970)
  covalent geometry    : angle       0.85073 /  0.46 (13514)
  hydrogen bonds       : bond        0.06335 /  4.39 (  595)
  hydrogen bonds       : angle       6.45813 /  4.72 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 338
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LEU cc_start: 0.8991 (mm) cc_final: 0.8751 (mm)
REVERT: A   98 TYR cc_start: 0.7667 (t80) cc_final: 0.7294 (t80)
REVERT: A  110 LYS cc_start: 0.9150 (tptt) cc_final: 0.8879 (tppp)
REVERT: A  116 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.8068 (mmt-90)
REVERT: A  132 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8469 (mtm180)
REVERT: A  153 PHE cc_start: 0.9211 (t80) cc_final: 0.8965 (t80)
REVERT: A  179 HIS cc_start: 0.8442 (m-70) cc_final: 0.8013 (m-70)
REVERT: A  211 LYS cc_start: 0.9163 (mttp) cc_final: 0.8937 (mttm)
REVERT: A  372 GLU cc_start: 0.9259 (mp0) cc_final: 0.8863 (mp0)
REVERT: A  376 LEU cc_start: 0.9684 (mm) cc_final: 0.9360 (mm)
REVERT: A  380 HIS cc_start: 0.9242 (m-70) cc_final: 0.8599 (m-70)
REVERT: B   29 LEU cc_start: 0.9130 (tp) cc_final: 0.8864 (tp)
REVERT: B   78 CYS cc_start: 0.8715 (p) cc_final: 0.8512 (p)
REVERT: B  137 MET cc_start: 0.8329 (tpt) cc_final: 0.7995 (tpt)
REVERT: B  179 HIS cc_start: 0.8808 (m-70) cc_final: 0.8422 (m-70)
REVERT: B  185 ILE cc_start: 0.8347 (tt) cc_final: 0.8136 (tt)
REVERT: B  192 GLN cc_start: 0.7440 (mt0) cc_final: 0.7073 (mp10)
REVERT: B  344 ARG cc_start: 0.9193 (ttt-90) cc_final: 0.8489 (mtp180)
REVERT: B  354 LEU cc_start: 0.9628 (mm) cc_final: 0.9388 (mm)
REVERT: B  363 LEU cc_start: 0.9353 (mt) cc_final: 0.9065 (mt)
REVERT: B  376 LEU cc_start: 0.9741 (mt) cc_final: 0.9397 (mt)
REVERT: B  377 MET cc_start: 0.9522 (ttm) cc_final: 0.9145 (mtp)
REVERT: B  380 HIS cc_start: 0.9129 (m90) cc_final: 0.8666 (m90)
REVERT: C   76 PHE cc_start: 0.9134 (m-80) cc_final: 0.8880 (m-80)
REVERT: C  159 LYS cc_start: 0.8061 (mttt) cc_final: 0.7780 (tptp)
REVERT: C  160 PHE cc_start: 0.8736 (t80) cc_final: 0.8178 (t80)
REVERT: C  163 LYS cc_start: 0.7322 (tttt) cc_final: 0.6529 (pttt)
REVERT: C  191 THR cc_start: 0.9131 (m) cc_final: 0.8740 (p)
REVERT: C  198 LEU cc_start: 0.9216 (tp) cc_final: 0.8902 (tp)
REVERT: C  200 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8055 (mt-10)
REVERT: C  213 LYS cc_start: 0.8954 (tttt) cc_final: 0.8596 (tmtt)
REVERT: C  222 LEU cc_start: 0.9403 (pp) cc_final: 0.8977 (tt)
REVERT: D   31 VAL cc_start: 0.9159 (p) cc_final: 0.8744 (p)
REVERT: D  115 LEU cc_start: 0.9314 (mt) cc_final: 0.8774 (tt)
REVERT: D  124 ASP cc_start: 0.9582 (m-30) cc_final: 0.9363 (m-30)
REVERT: D  126 LEU cc_start: 0.9807 (mt) cc_final: 0.9594 (mt)
REVERT: D  149 MET cc_start: 0.9180 (mpp) cc_final: 0.8874 (mpp)
REVERT: D  187 THR cc_start: 0.8536 (m) cc_final: 0.8125 (p)
REVERT: D  219 PHE cc_start: 0.7169 (p90) cc_final: 0.6960 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 338
  average time/residue: 0.0734
  time to fit residues: 34.8310
Evaluate side-chains
  289 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 69 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 80 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0270
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 109 optimal weight:    9.9990
   overall best weight:    2.0642

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 225 HIS
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  51 HIS
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.123543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.098635 restraints weight = 32501.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.101934 restraints weight = 21968.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.104396 restraints weight = 16178.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.106227 restraints weight = 12636.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.107664 restraints weight = 10329.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.5916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   9970  Z= 0.194
  Angle     :  0.842  11.701  13514  Z= 0.453
  Chirality :  0.047   0.258   1563
  Planarity :  0.007   0.160   1689
  Dihedral  : 11.356 126.667   1464
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.61 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.30 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.43 %

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: -1.20 (0.23), residues: 1197
  helix: -0.07 (0.19), residues: 689
  sheet:  0.80 (0.46), residues: 110
  loop : -2.51 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  95 
 TYR   0.027   0.002   TYR B  98 
 PHE   0.033   0.003   PHE B  66 
 TRP   0.029   0.002   TRP D  92 
 HIS   0.034   0.002   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.19 ( 9970)
  covalent geometry    : angle       0.84221 /  0.45 (13514)
  hydrogen bonds       : bond        0.06181 /  4.31 (  595)
  hydrogen bonds       : angle       6.35719 /  4.63 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 341
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.9093 (ptp) cc_final: 0.8767 (ppp)
REVERT: A   77 LEU cc_start: 0.9235 (mt) cc_final: 0.8544 (mt)
REVERT: A  110 LYS cc_start: 0.9131 (tptt) cc_final: 0.8927 (tppp)
REVERT: A  116 ARG cc_start: 0.8313 (mmt-90) cc_final: 0.7979 (mmt-90)
REVERT: A  132 ARG cc_start: 0.8739 (mtm110) cc_final: 0.8455 (mtm180)
REVERT: A  153 PHE cc_start: 0.9158 (t80) cc_final: 0.8790 (t80)
REVERT: A  179 HIS cc_start: 0.8365 (m-70) cc_final: 0.7950 (m-70)
REVERT: A  244 LEU cc_start: 0.5803 (mt) cc_final: 0.4615 (mm)
REVERT: A  372 GLU cc_start: 0.9259 (mp0) cc_final: 0.8850 (mp0)
REVERT: A  376 LEU cc_start: 0.9696 (mm) cc_final: 0.9240 (mm)
REVERT: A  377 MET cc_start: 0.9151 (tmm) cc_final: 0.8822 (tmm)
REVERT: A  380 HIS cc_start: 0.9324 (m-70) cc_final: 0.8615 (m90)
REVERT: B   21 TYR cc_start: 0.7507 (m-80) cc_final: 0.7296 (m-80)
REVERT: B   54 GLN cc_start: 0.9509 (pp30) cc_final: 0.9123 (pp30)
REVERT: B   55 LEU cc_start: 0.9217 (mt) cc_final: 0.8805 (mt)
REVERT: B   74 LEU cc_start: 0.9407 (mt) cc_final: 0.9195 (mt)
REVERT: B   78 CYS cc_start: 0.8706 (p) cc_final: 0.8485 (p)
REVERT: B  137 MET cc_start: 0.8305 (tpt) cc_final: 0.7987 (tpt)
REVERT: B  179 HIS cc_start: 0.8772 (m-70) cc_final: 0.8474 (m-70)
REVERT: B  192 GLN cc_start: 0.7406 (mt0) cc_final: 0.7163 (mp10)
REVERT: B  196 HIS cc_start: 0.8407 (m-70) cc_final: 0.8161 (m-70)
REVERT: B  307 ASN cc_start: 0.7923 (m-40) cc_final: 0.7535 (t0)
REVERT: B  344 ARG cc_start: 0.9225 (ttt-90) cc_final: 0.8485 (mtp180)
REVERT: B  354 LEU cc_start: 0.9640 (mm) cc_final: 0.9412 (mm)
REVERT: B  363 LEU cc_start: 0.9362 (mt) cc_final: 0.9024 (mt)
REVERT: B  376 LEU cc_start: 0.9694 (mt) cc_final: 0.9277 (mt)
REVERT: B  377 MET cc_start: 0.9481 (ttm) cc_final: 0.9108 (mtp)
REVERT: B  380 HIS cc_start: 0.9090 (m90) cc_final: 0.8762 (m90)
REVERT: C  159 LYS cc_start: 0.7963 (mttt) cc_final: 0.7660 (tptp)
REVERT: C  160 PHE cc_start: 0.8686 (t80) cc_final: 0.8074 (t80)
REVERT: C  163 LYS cc_start: 0.7237 (tttt) cc_final: 0.6463 (pttt)
REVERT: C  198 LEU cc_start: 0.9218 (tp) cc_final: 0.9016 (tp)
REVERT: C  213 LYS cc_start: 0.8944 (tttt) cc_final: 0.8603 (tmtt)
REVERT: C  222 LEU cc_start: 0.9264 (pp) cc_final: 0.8966 (tt)
REVERT: D   31 VAL cc_start: 0.8790 (p) cc_final: 0.8524 (p)
REVERT: D  109 GLN cc_start: 0.7893 (tt0) cc_final: 0.7486 (tp-100)
REVERT: D  124 ASP cc_start: 0.9631 (m-30) cc_final: 0.9378 (m-30)
REVERT: D  147 LEU cc_start: 0.8620 (mt) cc_final: 0.8258 (mt)
REVERT: D  149 MET cc_start: 0.9224 (mpp) cc_final: 0.8459 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 341
  average time/residue: 0.0754
  time to fit residues: 36.3398
Evaluate side-chains
  280 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 52 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 104 optimal weight:   10.0000
   chunk 101 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    4.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 GLN
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.117145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.094100 restraints weight = 32815.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.097217 restraints weight = 21759.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.099446 restraints weight = 15833.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.101100 restraints weight = 12303.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.102443 restraints weight = 10026.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.6185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   9970  Z= 0.288
  Angle     :  0.943  11.997  13514  Z= 0.504
  Chirality :  0.050   0.263   1563
  Planarity :  0.008   0.161   1689
  Dihedral  : 11.508 119.774   1464
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 26.16
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 11.03 %
    Favored  : 88.55 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.07 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.43 %

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: -1.75 (0.23), residues: 1197
  helix: -0.49 (0.18), residues: 680
  sheet:  0.41 (0.48), residues: 106
  loop : -2.66 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  95 
 TYR   0.029   0.003   TYR B  98 
 PHE   0.043   0.004   PHE B  66 
 TRP   0.023   0.003   TRP D  69 
 HIS   0.026   0.003   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00579 /  0.29 ( 9970)
  covalent geometry    : angle       0.94258 /  0.50 (13514)
  hydrogen bonds       : bond        0.06450 /  4.46 (  595)
  hydrogen bonds       : angle       6.62998 /  4.84 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 320
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 ARG cc_start: 0.8383 (mmt-90) cc_final: 0.7680 (mmp80)
REVERT: A  132 ARG cc_start: 0.8721 (mtm110) cc_final: 0.8312 (mtm180)
REVERT: A  153 PHE cc_start: 0.9243 (t80) cc_final: 0.8866 (t80)
REVERT: A  179 HIS cc_start: 0.8489 (m-70) cc_final: 0.8125 (m-70)
REVERT: A  201 PHE cc_start: 0.8438 (m-80) cc_final: 0.8211 (m-80)
REVERT: A  364 ASP cc_start: 0.8378 (t0) cc_final: 0.8150 (p0)
REVERT: A  372 GLU cc_start: 0.9274 (mp0) cc_final: 0.8939 (mp0)
REVERT: A  384 ASN cc_start: 0.9665 (m110) cc_final: 0.9366 (m110)
REVERT: B   55 LEU cc_start: 0.9199 (mt) cc_final: 0.8809 (mt)
REVERT: B   78 CYS cc_start: 0.8801 (p) cc_final: 0.8548 (p)
REVERT: B   88 LYS cc_start: 0.9500 (tttt) cc_final: 0.9157 (tptp)
REVERT: B  137 MET cc_start: 0.8299 (tpt) cc_final: 0.7972 (tpt)
REVERT: B  192 GLN cc_start: 0.7442 (mt0) cc_final: 0.7173 (mp10)
REVERT: B  196 HIS cc_start: 0.8252 (m-70) cc_final: 0.7989 (m-70)
REVERT: B  198 MET cc_start: 0.8658 (mmm) cc_final: 0.8311 (mmm)
REVERT: B  354 LEU cc_start: 0.9564 (mm) cc_final: 0.9340 (mm)
REVERT: B  363 LEU cc_start: 0.9379 (mt) cc_final: 0.9071 (mt)
REVERT: B  376 LEU cc_start: 0.9745 (mt) cc_final: 0.9258 (mt)
REVERT: B  377 MET cc_start: 0.9449 (ttm) cc_final: 0.9087 (mtp)
REVERT: B  380 HIS cc_start: 0.9048 (m90) cc_final: 0.8631 (m90)
REVERT: B  382 LYS cc_start: 0.9753 (mmmm) cc_final: 0.9480 (mmmm)
REVERT: C   76 PHE cc_start: 0.9194 (m-80) cc_final: 0.8925 (m-80)
REVERT: C  159 LYS cc_start: 0.7990 (mttt) cc_final: 0.7703 (tptp)
REVERT: C  160 PHE cc_start: 0.8793 (t80) cc_final: 0.8221 (t80)
REVERT: C  163 LYS cc_start: 0.7479 (tttt) cc_final: 0.6680 (pttt)
REVERT: C  200 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8853 (mt-10)
REVERT: C  213 LYS cc_start: 0.9045 (tttt) cc_final: 0.8721 (tmtt)
REVERT: C  222 LEU cc_start: 0.9259 (pp) cc_final: 0.9005 (tt)
REVERT: D   31 VAL cc_start: 0.8930 (p) cc_final: 0.8612 (p)
REVERT: D  124 ASP cc_start: 0.9627 (m-30) cc_final: 0.9302 (m-30)
REVERT: D  149 MET cc_start: 0.9303 (mpp) cc_final: 0.8847 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 321
  average time/residue: 0.0764
  time to fit residues: 34.3908
Evaluate side-chains
  272 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.1980
   chunk 109 optimal weight:    0.0870
   chunk 98 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0470
   chunk 86 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.4056

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 335 ASN
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 GLN
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.126270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.102415 restraints weight = 30836.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.105734 restraints weight = 20383.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.108212 restraints weight = 14729.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.110125 restraints weight = 11300.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.111500 restraints weight = 9039.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.6581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9970  Z= 0.178
  Angle     :  0.854  11.308  13514  Z= 0.455
  Chirality :  0.047   0.251   1563
  Planarity :  0.007   0.155   1689
  Dihedral  : 11.101 115.930   1464
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.61 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.23), residues: 1197
  helix: -0.29 (0.19), residues: 694
  sheet:  0.74 (0.50), residues: 106
  loop : -2.49 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  95 
 TYR   0.025   0.002   TYR B  98 
 PHE   0.039   0.003   PHE B  66 
 TRP   0.024   0.002   TRP D  92 
 HIS   0.023   0.002   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.18 ( 9970)
  covalent geometry    : angle       0.85367 /  0.45 (13514)
  hydrogen bonds       : bond        0.05788 /  4.03 (  595)
  hydrogen bonds       : angle       6.27125 /  4.58 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 364
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ILE cc_start: 0.8986 (tp) cc_final: 0.8773 (tp)
REVERT: A   76 MET cc_start: 0.9192 (ptp) cc_final: 0.8931 (ppp)
REVERT: A   77 LEU cc_start: 0.9187 (mt) cc_final: 0.8454 (mt)
REVERT: A   98 TYR cc_start: 0.7770 (t80) cc_final: 0.7441 (t80)
REVERT: A  153 PHE cc_start: 0.9108 (t80) cc_final: 0.8757 (t80)
REVERT: A  179 HIS cc_start: 0.8293 (m-70) cc_final: 0.7968 (m-70)
REVERT: A  248 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8610 (ttpt)
REVERT: A  372 GLU cc_start: 0.9209 (mp0) cc_final: 0.8805 (mp0)
REVERT: A  377 MET cc_start: 0.9073 (tmm) cc_final: 0.8801 (tmm)
REVERT: B   19 MET cc_start: 0.8326 (pmm) cc_final: 0.7723 (pmm)
REVERT: B   54 GLN cc_start: 0.9550 (pp30) cc_final: 0.9227 (pp30)
REVERT: B   55 LEU cc_start: 0.9119 (mt) cc_final: 0.8699 (mt)
REVERT: B   74 LEU cc_start: 0.9396 (mt) cc_final: 0.9180 (mt)
REVERT: B   78 CYS cc_start: 0.8644 (p) cc_final: 0.8443 (p)
REVERT: B   88 LYS cc_start: 0.9470 (tttt) cc_final: 0.9120 (tptp)
REVERT: B  170 GLU cc_start: 0.8884 (pp20) cc_final: 0.8594 (tm-30)
REVERT: B  179 HIS cc_start: 0.8735 (m-70) cc_final: 0.8395 (m-70)
REVERT: B  192 GLN cc_start: 0.7378 (mt0) cc_final: 0.7016 (mp10)
REVERT: B  196 HIS cc_start: 0.8274 (m-70) cc_final: 0.7937 (m-70)
REVERT: B  197 MET cc_start: 0.6801 (ptp) cc_final: 0.6494 (ptp)
REVERT: B  198 MET cc_start: 0.8359 (mmm) cc_final: 0.7974 (mmm)
REVERT: B  307 ASN cc_start: 0.7754 (m-40) cc_final: 0.7438 (t0)
REVERT: B  343 LEU cc_start: 0.9498 (mp) cc_final: 0.9272 (mm)
REVERT: B  344 ARG cc_start: 0.9266 (ttt-90) cc_final: 0.8546 (mtp180)
REVERT: B  354 LEU cc_start: 0.9578 (mm) cc_final: 0.9317 (mm)
REVERT: B  363 LEU cc_start: 0.9333 (mt) cc_final: 0.9006 (mt)
REVERT: B  366 LEU cc_start: 0.7843 (tp) cc_final: 0.7521 (tt)
REVERT: B  376 LEU cc_start: 0.9690 (mt) cc_final: 0.9253 (mt)
REVERT: B  377 MET cc_start: 0.9427 (ttm) cc_final: 0.9104 (mtp)
REVERT: B  380 HIS cc_start: 0.9048 (m90) cc_final: 0.8745 (m90)
REVERT: B  382 LYS cc_start: 0.9795 (mmmm) cc_final: 0.9460 (mmmm)
REVERT: C   42 TRP cc_start: 0.8546 (t60) cc_final: 0.8294 (t-100)
REVERT: C  160 PHE cc_start: 0.8762 (t80) cc_final: 0.8462 (t80)
REVERT: C  213 LYS cc_start: 0.8885 (tttt) cc_final: 0.8530 (tmtt)
REVERT: C  222 LEU cc_start: 0.9221 (pp) cc_final: 0.9012 (tt)
REVERT: D  124 ASP cc_start: 0.9648 (m-30) cc_final: 0.9367 (m-30)
REVERT: D  147 LEU cc_start: 0.8754 (mt) cc_final: 0.8490 (mt)
REVERT: D  149 MET cc_start: 0.9211 (mpp) cc_final: 0.8406 (mpp)
REVERT: D  212 MET cc_start: 0.5983 (ttm) cc_final: 0.5097 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 364
  average time/residue: 0.0715
  time to fit residues: 37.2167
Evaluate side-chains
  283 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.0980
   chunk 68 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 43 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 GLN
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.126514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.101863 restraints weight = 31347.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.105222 restraints weight = 20931.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.107717 restraints weight = 15266.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.109619 restraints weight = 11793.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.111048 restraints weight = 9521.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.6945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   9970  Z= 0.180
  Angle     :  0.865  13.463  13514  Z= 0.463
  Chirality :  0.049   0.253   1563
  Planarity :  0.007   0.153   1689
  Dihedral  : 10.908 112.782   1464
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.86 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.09 %

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: -1.47 (0.24), residues: 1197
  helix: -0.37 (0.19), residues: 695
  sheet:  0.81 (0.50), residues: 106
  loop : -2.50 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  95 
 TYR   0.026   0.002   TYR B  98 
 PHE   0.040   0.003   PHE B  66 
 TRP   0.018   0.002   TRP D  92 
 HIS   0.019   0.002   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.18 ( 9970)
  covalent geometry    : angle       0.86544 /  0.46 (13514)
  hydrogen bonds       : bond        0.05762 /  3.97 (  595)
  hydrogen bonds       : angle       6.35976 /  4.63 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 350
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.9173 (ptp) cc_final: 0.8251 (tmm)
REVERT: A   77 LEU cc_start: 0.9204 (mt) cc_final: 0.8610 (mt)
REVERT: A   80 HIS cc_start: 0.7777 (m170) cc_final: 0.7224 (m170)
REVERT: A   88 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8313 (tppt)
REVERT: A   98 TYR cc_start: 0.7618 (t80) cc_final: 0.7408 (t80)
REVERT: A  146 ASN cc_start: 0.8748 (p0) cc_final: 0.8404 (m110)
REVERT: A  153 PHE cc_start: 0.9039 (t80) cc_final: 0.8715 (t80)
REVERT: A  179 HIS cc_start: 0.8323 (m-70) cc_final: 0.7969 (m-70)
REVERT: A  372 GLU cc_start: 0.9181 (mp0) cc_final: 0.8802 (mp0)
REVERT: A  377 MET cc_start: 0.9071 (tmm) cc_final: 0.8855 (tmm)
REVERT: B   19 MET cc_start: 0.8329 (pmm) cc_final: 0.7562 (pmm)
REVERT: B   55 LEU cc_start: 0.9106 (mt) cc_final: 0.8843 (mt)
REVERT: B   74 LEU cc_start: 0.9407 (mt) cc_final: 0.9197 (mt)
REVERT: B   78 CYS cc_start: 0.8794 (p) cc_final: 0.8577 (p)
REVERT: B   88 LYS cc_start: 0.9445 (tttt) cc_final: 0.9100 (tptp)
REVERT: B  100 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8454 (mm-30)
REVERT: B  110 LYS cc_start: 0.9431 (mmpt) cc_final: 0.9105 (tppt)
REVERT: B  157 PHE cc_start: 0.8334 (m-80) cc_final: 0.7655 (m-10)
REVERT: B  179 HIS cc_start: 0.8613 (m-70) cc_final: 0.8336 (m-70)
REVERT: B  187 TYR cc_start: 0.7273 (t80) cc_final: 0.6728 (t80)
REVERT: B  189 THR cc_start: 0.6489 (p) cc_final: 0.5442 (p)
REVERT: B  198 MET cc_start: 0.8403 (mmm) cc_final: 0.7946 (mmm)
REVERT: B  307 ASN cc_start: 0.7889 (m-40) cc_final: 0.7626 (t0)
REVERT: B  344 ARG cc_start: 0.9421 (ttt-90) cc_final: 0.8908 (mmm-85)
REVERT: B  354 LEU cc_start: 0.9563 (mm) cc_final: 0.9299 (mm)
REVERT: B  363 LEU cc_start: 0.9363 (mt) cc_final: 0.9041 (mt)
REVERT: B  376 LEU cc_start: 0.9697 (mt) cc_final: 0.9257 (mt)
REVERT: B  377 MET cc_start: 0.9457 (ttm) cc_final: 0.9152 (mtp)
REVERT: B  380 HIS cc_start: 0.9097 (m90) cc_final: 0.8886 (m90)
REVERT: B  382 LYS cc_start: 0.9791 (mmmm) cc_final: 0.9399 (mmmm)
REVERT: C   42 TRP cc_start: 0.8541 (t60) cc_final: 0.8324 (t-100)
REVERT: C  213 LYS cc_start: 0.8865 (tttt) cc_final: 0.8519 (tmtt)
REVERT: D  104 ASP cc_start: 0.8751 (t70) cc_final: 0.8489 (t0)
REVERT: D  124 ASP cc_start: 0.9692 (m-30) cc_final: 0.9432 (m-30)
REVERT: D  147 LEU cc_start: 0.8736 (mt) cc_final: 0.8443 (mt)
REVERT: D  149 MET cc_start: 0.9191 (mpp) cc_final: 0.8338 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 350
  average time/residue: 0.0717
  time to fit residues: 35.6631
Evaluate side-chains
  281 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 114 optimal weight:    0.0770
   chunk 73 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   chunk 88 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.7942

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 GLN
** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.127154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.101921 restraints weight = 31479.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.105269 restraints weight = 21086.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.107760 restraints weight = 15461.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.109650 restraints weight = 12006.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.111007 restraints weight = 9767.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.7292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   9970  Z= 0.182
  Angle     :  0.876  16.923  13514  Z= 0.466
  Chirality :  0.049   0.286   1563
  Planarity :  0.007   0.152   1689
  Dihedral  : 10.831 109.185   1464
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 19.63
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  9.36 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

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: -1.52 (0.24), residues: 1197
  helix: -0.40 (0.19), residues: 698
  sheet:  0.65 (0.48), residues: 111
  loop : -2.53 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 398 
 TYR   0.025   0.002   TYR B  98 
 PHE   0.038   0.003   PHE B 157 
 TRP   0.030   0.002   TRP B 191 
 HIS   0.008   0.001   HIS C  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.18 ( 9970)
  covalent geometry    : angle       0.87613 /  0.47 (13514)
  hydrogen bonds       : bond        0.05694 /  3.93 (  595)
  hydrogen bonds       : angle       6.29840 /  4.60 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 336
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 TYR cc_start: 0.5609 (m-80) cc_final: 0.5334 (m-80)
REVERT: A   98 TYR cc_start: 0.7637 (t80) cc_final: 0.7434 (t80)
REVERT: A  109 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8458 (ttpp)
REVERT: A  153 PHE cc_start: 0.9018 (t80) cc_final: 0.8708 (t80)
REVERT: A  179 HIS cc_start: 0.8266 (m-70) cc_final: 0.7977 (m-70)
REVERT: A  248 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8585 (mtpt)
REVERT: A  372 GLU cc_start: 0.9178 (mp0) cc_final: 0.8820 (mp0)
REVERT: A  384 ASN cc_start: 0.9646 (m110) cc_final: 0.9356 (m110)
REVERT: A  394 MET cc_start: 0.9345 (mmm) cc_final: 0.9076 (mmm)
REVERT: B   19 MET cc_start: 0.8352 (pmm) cc_final: 0.7285 (pmm)
REVERT: B   55 LEU cc_start: 0.9143 (mt) cc_final: 0.8898 (mt)
REVERT: B   74 LEU cc_start: 0.9369 (mt) cc_final: 0.9122 (mt)
REVERT: B   78 CYS cc_start: 0.8772 (p) cc_final: 0.8564 (p)
REVERT: B   88 LYS cc_start: 0.9462 (tttt) cc_final: 0.9094 (tptp)
REVERT: B  100 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8646 (tp30)
REVERT: B  110 LYS cc_start: 0.9426 (mmpt) cc_final: 0.9117 (tppt)
REVERT: B  179 HIS cc_start: 0.8663 (m-70) cc_final: 0.8368 (m-70)
REVERT: B  187 TYR cc_start: 0.7762 (t80) cc_final: 0.7456 (t80)
REVERT: B  197 MET cc_start: 0.6915 (ptp) cc_final: 0.6350 (ptp)
REVERT: B  198 MET cc_start: 0.8408 (mmm) cc_final: 0.7928 (mmm)
REVERT: B  307 ASN cc_start: 0.7842 (m-40) cc_final: 0.7629 (t0)
REVERT: B  344 ARG cc_start: 0.9414 (ttt-90) cc_final: 0.8916 (mmm-85)
REVERT: B  363 LEU cc_start: 0.9378 (mt) cc_final: 0.9008 (mt)
REVERT: B  376 LEU cc_start: 0.9698 (mt) cc_final: 0.9281 (mt)
REVERT: B  380 HIS cc_start: 0.9149 (m90) cc_final: 0.8905 (m90)
REVERT: B  381 GLN cc_start: 0.9471 (pt0) cc_final: 0.9253 (pt0)
REVERT: B  382 LYS cc_start: 0.9794 (mmmm) cc_final: 0.9399 (mmmm)
REVERT: C   48 ASP cc_start: 0.8268 (p0) cc_final: 0.7942 (p0)
REVERT: C  159 LYS cc_start: 0.8778 (mmtp) cc_final: 0.8345 (ptmm)
REVERT: C  160 PHE cc_start: 0.8725 (t80) cc_final: 0.8221 (t80)
REVERT: C  163 LYS cc_start: 0.7448 (tttt) cc_final: 0.6942 (pttt)
REVERT: C  213 LYS cc_start: 0.8828 (tttt) cc_final: 0.8492 (tmtt)
REVERT: D  124 ASP cc_start: 0.9700 (m-30) cc_final: 0.9448 (m-30)
REVERT: D  136 MET cc_start: 0.6945 (mmp) cc_final: 0.6610 (mmm)
REVERT: D  149 MET cc_start: 0.9290 (mpp) cc_final: 0.9011 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 336
  average time/residue: 0.0735
  time to fit residues: 34.9675
Evaluate side-chains
  273 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0070
   chunk 53 optimal weight:    0.2980
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0040
   chunk 70 optimal weight:    0.6980
   chunk 105 optimal weight:    0.5980
   chunk 73 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.3210

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 ASN
D  81 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 GLN
** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.129017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.103436 restraints weight = 30978.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.106774 restraints weight = 20926.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.109296 restraints weight = 15403.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.111149 restraints weight = 12021.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.112550 restraints weight = 9844.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.7569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   9970  Z= 0.175
  Angle     :  0.873  20.199  13514  Z= 0.464
  Chirality :  0.048   0.261   1563
  Planarity :  0.007   0.151   1689
  Dihedral  : 10.728 105.231   1464
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  9.44 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

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: -1.43 (0.24), residues: 1197
  helix: -0.39 (0.19), residues: 695
  sheet:  0.69 (0.56), residues: 91
  loop : -2.20 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 398 
 TYR   0.024   0.002   TYR B  98 
 PHE   0.042   0.003   PHE B  66 
 TRP   0.030   0.002   TRP B 191 
 HIS   0.027   0.002   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.18 ( 9970)
  covalent geometry    : angle       0.87283 /  0.46 (13514)
  hydrogen bonds       : bond        0.05597 /  3.87 (  595)
  hydrogen bonds       : angle       6.30497 /  4.57 ( 1728)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 350
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.9136 (ptp) cc_final: 0.8892 (ppp)
REVERT: A   77 LEU cc_start: 0.9213 (mt) cc_final: 0.8504 (mt)
REVERT: A  109 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8401 (ttpp)
REVERT: A  153 PHE cc_start: 0.8977 (t80) cc_final: 0.8663 (t80)
REVERT: A  174 ARG cc_start: 0.9137 (mtp180) cc_final: 0.8433 (mtp180)
REVERT: A  200 ILE cc_start: 0.9124 (tt) cc_final: 0.8893 (tt)
REVERT: A  211 LYS cc_start: 0.9208 (mttp) cc_final: 0.9006 (mttm)
REVERT: A  248 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8665 (tppt)
REVERT: A  372 GLU cc_start: 0.9144 (mp0) cc_final: 0.8840 (mp0)
REVERT: A  384 ASN cc_start: 0.9648 (m110) cc_final: 0.9332 (m110)
REVERT: A  394 MET cc_start: 0.9330 (mmm) cc_final: 0.9068 (mmm)
REVERT: B   19 MET cc_start: 0.8286 (pmm) cc_final: 0.7282 (pmm)
REVERT: B   20 ASP cc_start: 0.7938 (m-30) cc_final: 0.6693 (m-30)
REVERT: B   55 LEU cc_start: 0.9070 (mt) cc_final: 0.8809 (mt)
REVERT: B   74 LEU cc_start: 0.9392 (mt) cc_final: 0.9164 (mt)
REVERT: B   78 CYS cc_start: 0.8829 (p) cc_final: 0.8626 (p)
REVERT: B   88 LYS cc_start: 0.9473 (tttt) cc_final: 0.9107 (tptp)
REVERT: B  110 LYS cc_start: 0.9429 (mmpt) cc_final: 0.9167 (tppt)
REVERT: B  174 ARG cc_start: 0.9387 (mtt180) cc_final: 0.9008 (ptp-170)
REVERT: B  179 HIS cc_start: 0.8539 (m-70) cc_final: 0.8237 (m-70)
REVERT: B  187 TYR cc_start: 0.7580 (t80) cc_final: 0.7237 (t80)
REVERT: B  192 GLN cc_start: 0.7233 (pm20) cc_final: 0.6434 (mp10)
REVERT: B  196 HIS cc_start: 0.8467 (m-70) cc_final: 0.7790 (m-70)
REVERT: B  198 MET cc_start: 0.8295 (mmm) cc_final: 0.7908 (mmm)
REVERT: B  363 LEU cc_start: 0.9338 (mt) cc_final: 0.8984 (mt)
REVERT: B  376 LEU cc_start: 0.9712 (mt) cc_final: 0.9315 (mt)
REVERT: B  380 HIS cc_start: 0.9164 (m90) cc_final: 0.8896 (m90)
REVERT: B  381 GLN cc_start: 0.9434 (pt0) cc_final: 0.9200 (pt0)
REVERT: B  382 LYS cc_start: 0.9796 (mmmm) cc_final: 0.9402 (mmmm)
REVERT: B  400 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9044 (mm-30)
REVERT: C   76 PHE cc_start: 0.9125 (m-80) cc_final: 0.8921 (m-80)
REVERT: C  160 PHE cc_start: 0.8721 (t80) cc_final: 0.8380 (t80)
REVERT: C  163 LYS cc_start: 0.7440 (tttt) cc_final: 0.6947 (pttt)
REVERT: C  213 LYS cc_start: 0.8782 (tttt) cc_final: 0.8426 (tmtt)
REVERT: D  124 ASP cc_start: 0.9665 (m-30) cc_final: 0.9430 (m-30)
REVERT: D  149 MET cc_start: 0.9216 (mpp) cc_final: 0.8656 (mpp)
REVERT: D  167 LEU cc_start: 0.6312 (tp) cc_final: 0.6101 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 350
  average time/residue: 0.0737
  time to fit residues: 36.4738
Evaluate side-chains
  283 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0870
   chunk 79 optimal weight:    0.0570
   chunk 49 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 175 GLN
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 ASN
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 GLN
C 156 ASN
C 194 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.129577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.103636 restraints weight = 32237.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.106859 restraints weight = 22014.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.109364 restraints weight = 16377.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.111186 restraints weight = 12861.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.112652 restraints weight = 10559.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.7825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9970  Z= 0.181
  Angle     :  0.896  14.567  13514  Z= 0.472
  Chirality :  0.049   0.279   1563
  Planarity :  0.007   0.152   1689
  Dihedral  : 10.689 100.606   1464
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.11 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

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: -1.47 (0.24), residues: 1197
  helix: -0.43 (0.19), residues: 695
  sheet:  0.73 (0.55), residues: 96
  loop : -2.27 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 398 
 TYR   0.023   0.002   TYR B  98 
 PHE   0.035   0.003   PHE B  66 
 TRP   0.032   0.002   TRP B 191 
 HIS   0.016   0.001   HIS B 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.18 ( 9970)
  covalent geometry    : angle       0.89555 /  0.47 (13514)
  hydrogen bonds       : bond        0.05593 /  3.85 (  595)
  hydrogen bonds       : angle       6.36045 /  4.62 ( 1728)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1485.33 seconds
wall clock time: 26 minutes 31.40 seconds (1591.40 seconds total)