Starting phenix.real_space_refine
on Wed Apr 30 19:35:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9j_39081/04_2025/8y9j_39081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9j_39081/04_2025/8y9j_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_39081/04_2025/8y9j_39081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9j_39081/04_2025/8y9j_39081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9j_39081/04_2025/8y9j_39081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9j_39081/04_2025/8y9j_39081.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.94, per 1000 atoms: 0.61
  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: 2.82
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.99
  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: 2.59

  Time building geometry restraints manager: 3.29 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.100
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
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= 0.765
  Angle     :  2.024  12.832  13514  Z= 1.393
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.142   0.026   TRP C  42 
 HIS   0.016   0.004   HIS D  58 
 PHE   0.162   0.021   PHE D 134 
 TYR   0.208   0.032   TYR B 340 
 ARG   0.014   0.001   ARG B 361 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18979 (  595)
  hydrogen bonds       : angle       8.88888 ( 1728)
  covalent geometry    : bond        0.01226 ( 9970)
  covalent geometry    : angle       2.02369 (13514)

*********************** 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  : 1.028 
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: 0.8506 (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: 0.8773 (ttp-110)
REVERT: B   19 MET cc_start: 0.6513 (pmm) cc_final: 0.5582 (pmm)
REVERT: B  157 PHE cc_start: 0.9471 (m-80) cc_final: 0.9123 (m-80)
REVERT: B  194 VAL cc_start: 0.8832 (t) cc_final: 0.8556 (t)
REVERT: B  196 HIS cc_start: 0.9204 (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: 0.9211 (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: 0.8965 (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: 0.7761 (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: 0.8750 (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: 0.2332
  time to fit residues: 144.9991
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  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 94 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  32 GLN
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN
B 149 GLN
B 175 GLN
B 220 HIS
B 228 ASN
B 306 ASN
** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN
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: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.127459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.101866 restraints weight = 31580.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.105213 restraints weight = 21541.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.107716 restraints weight = 15932.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   9970  Z= 0.202
  Angle     :  0.913  13.989  13514  Z= 0.493
  Chirality :  0.049   0.251   1563
  Planarity :  0.007   0.170   1689
  Dihedral  : 12.517 137.585   1464
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  8.10 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  4.07 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.60 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.23), residues: 1197
  helix:  0.10 (0.18), residues: 686
  sheet:  0.74 (0.46), residues: 112
  loop : -2.56 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C  92 
 HIS   0.010   0.002   HIS C 223 
 PHE   0.038   0.003   PHE B  66 
 TYR   0.036   0.003   TYR A  44 
 ARG   0.006   0.001   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06845 (  595)
  hydrogen bonds       : angle       6.66048 ( 1728)
  covalent geometry    : bond        0.00401 ( 9970)
  covalent geometry    : angle       0.91347 (13514)

*********************** 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
  403 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 398
  time to evaluate  : 1.103 
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: symmetry clash
   revert: symmetry clash
REVERT: A   79 LEU cc_start: 0.9015 (mm) cc_final: 0.8797 (mm)
REVERT: A  110 LYS cc_start: 0.9261 (tptm) cc_final: 0.8928 (tppp)
REVERT: A  116 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7753 (mmp80)
REVERT: A  153 PHE cc_start: 0.9083 (t80) cc_final: 0.8428 (t80)
REVERT: A  179 HIS cc_start: 0.8535 (m-70) cc_final: 0.8183 (m-70)
REVERT: A  213 LEU cc_start: 0.9421 (tt) cc_final: 0.9179 (tt)
REVERT: A  308 LEU cc_start: 0.8687 (mm) cc_final: 0.8455 (mm)
REVERT: A  356 GLN cc_start: 0.9358 (mt0) cc_final: 0.9105 (mm110)
REVERT: A  359 GLU cc_start: 0.9250 (tt0) cc_final: 0.8995 (mt-10)
REVERT: A  362 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9282 (pp20)
REVERT: A  372 GLU cc_start: 0.9450 (mp0) cc_final: 0.9158 (mp0)
REVERT: A  376 LEU cc_start: 0.9739 (mm) cc_final: 0.9297 (mm)
REVERT: A  380 HIS cc_start: 0.9361 (m-70) cc_final: 0.8774 (m90)
REVERT: B   19 MET cc_start: 0.7590 (pmm) cc_final: 0.6886 (pmm)
REVERT: B   76 MET cc_start: 0.9279 (ptp) cc_final: 0.8985 (ptt)
REVERT: B   78 CYS cc_start: 0.8519 (p) cc_final: 0.8284 (p)
REVERT: B  221 MET cc_start: 0.7932 (ptm) cc_final: 0.7646 (ppp)
REVERT: B  363 LEU cc_start: 0.9297 (mt) cc_final: 0.9093 (mt)
REVERT: B  366 LEU cc_start: 0.7763 (tp) cc_final: 0.7513 (tt)
REVERT: B  376 LEU cc_start: 0.9694 (mt) cc_final: 0.9301 (mt)
REVERT: B  380 HIS cc_start: 0.9284 (m90) cc_final: 0.8838 (m90)
REVERT: C   42 TRP cc_start: 0.8464 (t60) cc_final: 0.7725 (t60)
REVERT: C   52 LYS cc_start: 0.6593 (mttm) cc_final: 0.6091 (mmtt)
REVERT: C  159 LYS cc_start: 0.8188 (mttt) cc_final: 0.7760 (tptp)
REVERT: C  160 PHE cc_start: 0.8752 (t80) cc_final: 0.8459 (t80)
REVERT: C  181 ILE cc_start: 0.8464 (mm) cc_final: 0.7848 (mm)
REVERT: C  191 THR cc_start: 0.9212 (m) cc_final: 0.8595 (p)
REVERT: C  198 LEU cc_start: 0.9178 (tp) cc_final: 0.8964 (tp)
REVERT: C  200 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8279 (mt-10)
REVERT: C  213 LYS cc_start: 0.8697 (tttt) cc_final: 0.8285 (pttt)
REVERT: C  222 LEU cc_start: 0.9445 (pp) cc_final: 0.9145 (tp)
REVERT: D   30 LEU cc_start: 0.8377 (mt) cc_final: 0.7654 (mp)
REVERT: D   92 TRP cc_start: 0.8656 (p-90) cc_final: 0.8261 (p-90)
REVERT: D  115 LEU cc_start: 0.9317 (mt) cc_final: 0.8679 (tt)
REVERT: D  119 LEU cc_start: 0.9660 (mt) cc_final: 0.9440 (mt)
REVERT: D  121 LEU cc_start: 0.9054 (mt) cc_final: 0.8683 (mt)
REVERT: D  124 ASP cc_start: 0.9544 (m-30) cc_final: 0.9138 (p0)
REVERT: D  149 MET cc_start: 0.9388 (mpp) cc_final: 0.9109 (mpp)
REVERT: D  152 LEU cc_start: 0.9498 (tp) cc_final: 0.9216 (tp)
REVERT: D  156 ASN cc_start: 0.9194 (m110) cc_final: 0.8918 (m110)
  outliers start: 5
  outliers final: 0
  residues processed: 398
  average time/residue: 0.2347
  time to fit residues: 128.3507
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  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0370
   chunk 61 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0670
   chunk 108 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A 192 GLN
A 196 HIS
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 GLN
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 353 GLN
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 202 GLN
** 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 = 0.4005 r_free = 0.4005 target = 0.129382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.104204 restraints weight = 31237.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.107670 restraints weight = 21051.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.110260 restraints weight = 15373.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.5488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   9970  Z= 0.178
  Angle     :  0.812  12.297  13514  Z= 0.444
  Chirality :  0.046   0.243   1563
  Planarity :  0.007   0.161   1689
  Dihedral  : 11.432 134.520   1464
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.77 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  4.56 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1197
  helix:  0.15 (0.19), residues: 688
  sheet:  1.01 (0.46), residues: 112
  loop : -2.38 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  69 
 HIS   0.030   0.001   HIS B 196 
 PHE   0.049   0.003   PHE B  66 
 TYR   0.024   0.002   TYR B  98 
 ARG   0.007   0.001   ARG A 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06078 (  595)
  hydrogen bonds       : angle       6.27709 ( 1728)
  covalent geometry    : bond        0.00358 ( 9970)
  covalent geometry    : angle       0.81167 (13514)

*********************** 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
  369 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 364
  time to evaluate  : 1.069 
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: A   19 MET cc_start: 0.8262 (pmm) cc_final: 0.8061 (pmm)
REVERT: A   79 LEU cc_start: 0.9039 (mm) cc_final: 0.8671 (mm)
REVERT: A  109 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8119 (ttpp)
REVERT: A  116 ARG cc_start: 0.8171 (mmt-90) cc_final: 0.7709 (mmp80)
REVERT: A  179 HIS cc_start: 0.8485 (m-70) cc_final: 0.8146 (m-70)
REVERT: A  204 MET cc_start: 0.8512 (tpp) cc_final: 0.8033 (tpp)
REVERT: A  211 LYS cc_start: 0.9107 (mttt) cc_final: 0.8502 (mttt)
REVERT: A  213 LEU cc_start: 0.9395 (tt) cc_final: 0.9064 (tt)
REVERT: A  240 ARG cc_start: 0.7868 (ttm110) cc_final: 0.6759 (mmm-85)
REVERT: A  248 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8631 (ttpt)
REVERT: A  252 ASP cc_start: 0.9323 (m-30) cc_final: 0.9080 (m-30)
REVERT: A  302 LEU cc_start: 0.5575 (mm) cc_final: 0.5293 (mp)
REVERT: A  351 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8615 (tm-30)
REVERT: A  376 LEU cc_start: 0.9658 (mm) cc_final: 0.9230 (mm)
REVERT: A  377 MET cc_start: 0.9230 (tmm) cc_final: 0.8740 (tmm)
REVERT: A  379 PHE cc_start: 0.9415 (t80) cc_final: 0.9074 (t80)
REVERT: A  380 HIS cc_start: 0.9242 (m-70) cc_final: 0.8563 (m90)
REVERT: B   19 MET cc_start: 0.7746 (pmm) cc_final: 0.7093 (pmm)
REVERT: B   54 GLN cc_start: 0.9475 (pp30) cc_final: 0.9177 (pp30)
REVERT: B   55 LEU cc_start: 0.9194 (mt) cc_final: 0.8771 (mt)
REVERT: B   57 ILE cc_start: 0.9165 (tt) cc_final: 0.8696 (tt)
REVERT: B   78 CYS cc_start: 0.8708 (p) cc_final: 0.8497 (p)
REVERT: B  196 HIS cc_start: 0.8402 (m-70) cc_final: 0.8080 (m-70)
REVERT: B  309 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8667 (mt-10)
REVERT: B  344 ARG cc_start: 0.9167 (ttt-90) cc_final: 0.8364 (mtp180)
REVERT: B  354 LEU cc_start: 0.9649 (mm) cc_final: 0.9369 (mm)
REVERT: B  363 LEU cc_start: 0.9351 (mt) cc_final: 0.8938 (mt)
REVERT: B  366 LEU cc_start: 0.7538 (tp) cc_final: 0.6768 (tt)
REVERT: B  376 LEU cc_start: 0.9695 (mt) cc_final: 0.9216 (mt)
REVERT: B  377 MET cc_start: 0.9522 (ttm) cc_final: 0.9101 (mtp)
REVERT: B  380 HIS cc_start: 0.9155 (m90) cc_final: 0.8926 (m90)
REVERT: C   42 TRP cc_start: 0.8412 (t60) cc_final: 0.7507 (t60)
REVERT: C   76 PHE cc_start: 0.8991 (m-80) cc_final: 0.8646 (m-80)
REVERT: C   91 LEU cc_start: 0.9297 (tp) cc_final: 0.8908 (tp)
REVERT: C  159 LYS cc_start: 0.8015 (mttt) cc_final: 0.7729 (tptp)
REVERT: C  160 PHE cc_start: 0.8885 (t80) cc_final: 0.8617 (t80)
REVERT: C  191 THR cc_start: 0.9100 (m) cc_final: 0.8545 (p)
REVERT: C  198 LEU cc_start: 0.9216 (tp) cc_final: 0.8951 (tp)
REVERT: C  200 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7971 (mt-10)
REVERT: C  222 LEU cc_start: 0.9305 (pp) cc_final: 0.8992 (tp)
REVERT: D   31 VAL cc_start: 0.8644 (p) cc_final: 0.8181 (p)
REVERT: D   46 GLU cc_start: 0.8441 (tt0) cc_final: 0.7772 (pm20)
REVERT: D  106 LEU cc_start: 0.9417 (mt) cc_final: 0.9216 (mt)
REVERT: D  109 GLN cc_start: 0.8855 (mp-120) cc_final: 0.8443 (mp10)
REVERT: D  124 ASP cc_start: 0.9632 (m-30) cc_final: 0.9318 (m-30)
REVERT: D  126 LEU cc_start: 0.9735 (mt) cc_final: 0.9526 (mt)
REVERT: D  149 MET cc_start: 0.9167 (mpp) cc_final: 0.8718 (mpp)
REVERT: D  165 ASP cc_start: 0.9067 (m-30) cc_final: 0.8790 (m-30)
REVERT: D  201 LEU cc_start: 0.8988 (tt) cc_final: 0.8487 (mp)
REVERT: D  212 MET cc_start: 0.4784 (ttt) cc_final: 0.4404 (ptt)
  outliers start: 5
  outliers final: 3
  residues processed: 368
  average time/residue: 0.2432
  time to fit residues: 121.7700
Evaluate side-chains
  297 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 294
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 67 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0270
   chunk 118 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 129 ASN
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 130 ASN
C 162 ASN
D 103 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 133 HIS
D 186 HIS
** 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.128443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.104025 restraints weight = 30231.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.107403 restraints weight = 20006.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.109927 restraints weight = 14500.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.6235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   9970  Z= 0.168
  Angle     :  0.794  11.313  13514  Z= 0.428
  Chirality :  0.046   0.247   1563
  Planarity :  0.007   0.160   1689
  Dihedral  : 10.979 132.151   1464
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  8.44 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.14 %
    Favored  : 94.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1197
  helix:  0.12 (0.19), residues: 686
  sheet:  0.74 (0.51), residues: 93
  loop : -2.06 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP D  92 
 HIS   0.025   0.002   HIS B 196 
 PHE   0.034   0.003   PHE B  66 
 TYR   0.022   0.002   TYR B  98 
 ARG   0.007   0.001   ARG A 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05679 (  595)
  hydrogen bonds       : angle       6.12619 ( 1728)
  covalent geometry    : bond        0.00343 ( 9970)
  covalent geometry    : angle       0.79417 (13514)

*********************** 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
  361 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 359
  time to evaluate  : 1.470 
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   19 MET cc_start: 0.8200 (pmm) cc_final: 0.7957 (pmm)
REVERT: A   76 MET cc_start: 0.9328 (ptt) cc_final: 0.8731 (tmm)
REVERT: A   77 LEU cc_start: 0.9121 (mt) cc_final: 0.8760 (mt)
REVERT: A   79 LEU cc_start: 0.8968 (mm) cc_final: 0.8764 (mm)
REVERT: A   80 HIS cc_start: 0.7951 (m170) cc_final: 0.7241 (m170)
REVERT: A  109 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8441 (ttpp)
REVERT: A  116 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7638 (mmp80)
REVERT: A  153 PHE cc_start: 0.9199 (t80) cc_final: 0.8779 (t80)
REVERT: A  200 ILE cc_start: 0.9445 (tp) cc_final: 0.9208 (tp)
REVERT: A  209 LEU cc_start: 0.9374 (pt) cc_final: 0.9158 (pt)
REVERT: A  211 LYS cc_start: 0.9261 (mttt) cc_final: 0.8978 (mttm)
REVERT: A  252 ASP cc_start: 0.9233 (m-30) cc_final: 0.9009 (m-30)
REVERT: A  364 ASP cc_start: 0.7894 (t0) cc_final: 0.7666 (p0)
REVERT: A  373 LYS cc_start: 0.9588 (tmmt) cc_final: 0.9134 (mttt)
REVERT: A  376 LEU cc_start: 0.9702 (mm) cc_final: 0.9243 (mm)
REVERT: A  377 MET cc_start: 0.9180 (tmm) cc_final: 0.8711 (tmm)
REVERT: A  379 PHE cc_start: 0.9358 (t80) cc_final: 0.9149 (t80)
REVERT: A  380 HIS cc_start: 0.9309 (m-70) cc_final: 0.8616 (m90)
REVERT: A  390 GLN cc_start: 0.9636 (mm110) cc_final: 0.9325 (mt0)
REVERT: B   19 MET cc_start: 0.7834 (pmm) cc_final: 0.7306 (pmm)
REVERT: B   78 CYS cc_start: 0.8787 (p) cc_final: 0.8540 (p)
REVERT: B  110 LYS cc_start: 0.8975 (mmpt) cc_final: 0.8691 (tppt)
REVERT: B  187 TYR cc_start: 0.7196 (t80) cc_final: 0.6606 (t80)
REVERT: B  198 MET cc_start: 0.8575 (mmm) cc_final: 0.8283 (mmm)
REVERT: B  307 ASN cc_start: 0.8225 (m110) cc_final: 0.7576 (t0)
REVERT: B  354 LEU cc_start: 0.9599 (mm) cc_final: 0.9386 (mm)
REVERT: B  363 LEU cc_start: 0.9338 (mt) cc_final: 0.9041 (mt)
REVERT: B  366 LEU cc_start: 0.7609 (tp) cc_final: 0.7026 (tt)
REVERT: B  376 LEU cc_start: 0.9721 (mt) cc_final: 0.9210 (mt)
REVERT: B  380 HIS cc_start: 0.9149 (m90) cc_final: 0.8938 (m90)
REVERT: C   58 HIS cc_start: 0.9223 (m170) cc_final: 0.9012 (m170)
REVERT: C   91 LEU cc_start: 0.9196 (tp) cc_final: 0.8833 (tp)
REVERT: C  160 PHE cc_start: 0.8839 (t80) cc_final: 0.8615 (t80)
REVERT: C  200 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8045 (mt-10)
REVERT: C  213 LYS cc_start: 0.8448 (tttp) cc_final: 0.7989 (tttp)
REVERT: C  218 LYS cc_start: 0.7295 (mppt) cc_final: 0.6747 (mppt)
REVERT: C  222 LEU cc_start: 0.9187 (pp) cc_final: 0.8926 (tt)
REVERT: D   46 GLU cc_start: 0.8655 (tt0) cc_final: 0.7606 (pm20)
REVERT: D  109 GLN cc_start: 0.8931 (mp-120) cc_final: 0.8532 (mp10)
REVERT: D  124 ASP cc_start: 0.9638 (m-30) cc_final: 0.9362 (m-30)
REVERT: D  126 LEU cc_start: 0.9766 (mt) cc_final: 0.9531 (mt)
REVERT: D  149 MET cc_start: 0.9082 (mpp) cc_final: 0.8614 (mpp)
REVERT: D  167 LEU cc_start: 0.6302 (tp) cc_final: 0.6026 (tp)
REVERT: D  212 MET cc_start: 0.4312 (ttt) cc_final: 0.3988 (ptt)
REVERT: D  219 PHE cc_start: 0.7110 (p90) cc_final: 0.5777 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 359
  average time/residue: 0.2523
  time to fit residues: 125.8625
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  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 115 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 113 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS
B 129 ASN
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 ASN
D  51 HIS
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.128998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.103655 restraints weight = 31530.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.106991 restraints weight = 21480.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.109471 restraints weight = 15839.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.6668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   9970  Z= 0.169
  Angle     :  0.805  12.359  13514  Z= 0.433
  Chirality :  0.047   0.251   1563
  Planarity :  0.007   0.157   1689
  Dihedral  : 10.802 128.978   1464
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  9.19 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.24), residues: 1197
  helix: -0.11 (0.19), residues: 702
  sheet:  0.65 (0.49), residues: 98
  loop : -2.11 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D  92 
 HIS   0.028   0.002   HIS B 196 
 PHE   0.033   0.003   PHE B  66 
 TYR   0.024   0.002   TYR B  98 
 ARG   0.005   0.000   ARG D  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05653 (  595)
  hydrogen bonds       : angle       6.05934 ( 1728)
  covalent geometry    : bond        0.00342 ( 9970)
  covalent geometry    : angle       0.80481 (13514)

*********************** 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
  345 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 345
  time to evaluate  : 1.335 
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   54 GLN cc_start: 0.9399 (mt0) cc_final: 0.9062 (mm-40)
REVERT: A   76 MET cc_start: 0.9304 (ptt) cc_final: 0.8635 (tmm)
REVERT: A   77 LEU cc_start: 0.9046 (mt) cc_final: 0.8685 (mt)
REVERT: A   79 LEU cc_start: 0.8983 (mm) cc_final: 0.8742 (mm)
REVERT: A   80 HIS cc_start: 0.7717 (m170) cc_final: 0.7158 (m170)
REVERT: A   98 TYR cc_start: 0.7724 (t80) cc_final: 0.7332 (t80)
REVERT: A  109 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8501 (ttpp)
REVERT: A  116 ARG cc_start: 0.8173 (mmt-90) cc_final: 0.7762 (mmp80)
REVERT: A  153 PHE cc_start: 0.9068 (t80) cc_final: 0.8694 (t80)
REVERT: A  174 ARG cc_start: 0.9221 (mtp180) cc_final: 0.8936 (mtp180)
REVERT: A  179 HIS cc_start: 0.8785 (m-70) cc_final: 0.8334 (m-70)
REVERT: A  211 LYS cc_start: 0.9452 (mttt) cc_final: 0.9082 (mttm)
REVERT: A  327 HIS cc_start: 0.7582 (m-70) cc_final: 0.5864 (m-70)
REVERT: A  376 LEU cc_start: 0.9699 (mm) cc_final: 0.9266 (mm)
REVERT: A  377 MET cc_start: 0.9210 (tmm) cc_final: 0.8807 (tmm)
REVERT: A  379 PHE cc_start: 0.9377 (t80) cc_final: 0.9148 (t80)
REVERT: A  380 HIS cc_start: 0.9336 (m-70) cc_final: 0.8724 (m90)
REVERT: A  390 GLN cc_start: 0.9658 (mm110) cc_final: 0.9242 (mt0)
REVERT: B   19 MET cc_start: 0.8152 (pmm) cc_final: 0.7487 (pmm)
REVERT: B   74 LEU cc_start: 0.9424 (mt) cc_final: 0.9221 (mt)
REVERT: B   78 CYS cc_start: 0.8745 (p) cc_final: 0.8516 (p)
REVERT: B  174 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8955 (mtm-85)
REVERT: B  187 TYR cc_start: 0.7220 (t80) cc_final: 0.6686 (t80)
REVERT: B  197 MET cc_start: 0.6852 (ptp) cc_final: 0.6340 (ptp)
REVERT: B  198 MET cc_start: 0.8483 (mmm) cc_final: 0.8142 (mmm)
REVERT: B  307 ASN cc_start: 0.8235 (m110) cc_final: 0.7807 (t0)
REVERT: B  354 LEU cc_start: 0.9537 (mm) cc_final: 0.9304 (mm)
REVERT: B  363 LEU cc_start: 0.9359 (mt) cc_final: 0.8973 (mt)
REVERT: B  366 LEU cc_start: 0.7413 (tp) cc_final: 0.6597 (tt)
REVERT: B  376 LEU cc_start: 0.9729 (mt) cc_final: 0.9192 (mt)
REVERT: B  377 MET cc_start: 0.9596 (ttm) cc_final: 0.9262 (ttm)
REVERT: C   42 TRP cc_start: 0.8447 (t-100) cc_final: 0.8086 (t-100)
REVERT: C   48 ASP cc_start: 0.7767 (p0) cc_final: 0.7371 (p0)
REVERT: C   58 HIS cc_start: 0.9238 (m170) cc_final: 0.9021 (m170)
REVERT: C   76 PHE cc_start: 0.9019 (m-80) cc_final: 0.8804 (m-80)
REVERT: C   88 GLU cc_start: 0.8675 (tp30) cc_final: 0.8471 (tp30)
REVERT: C   91 LEU cc_start: 0.9076 (tp) cc_final: 0.8704 (tp)
REVERT: C   94 LEU cc_start: 0.8995 (tp) cc_final: 0.8774 (tp)
REVERT: C  149 MET cc_start: 0.6147 (ptt) cc_final: 0.5690 (ppp)
REVERT: C  159 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8664 (ttpp)
REVERT: C  191 THR cc_start: 0.8917 (m) cc_final: 0.8506 (p)
REVERT: C  198 LEU cc_start: 0.9104 (tp) cc_final: 0.8684 (tp)
REVERT: C  200 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7718 (mt-10)
REVERT: D   71 MET cc_start: 0.4876 (mtp) cc_final: 0.4455 (ttt)
REVERT: D  124 ASP cc_start: 0.9639 (m-30) cc_final: 0.9381 (m-30)
REVERT: D  147 LEU cc_start: 0.8398 (mt) cc_final: 0.8072 (mt)
REVERT: D  149 MET cc_start: 0.8915 (mpp) cc_final: 0.8309 (mpp)
REVERT: D  209 MET cc_start: 0.1550 (ppp) cc_final: 0.1336 (ppp)
REVERT: D  212 MET cc_start: 0.3943 (ttt) cc_final: 0.3575 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 345
  average time/residue: 0.2073
  time to fit residues: 98.9673
Evaluate side-chains
  278 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 64 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 ASN
B 129 ASN
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 210 ASN
** D  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.127173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.101838 restraints weight = 31877.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.105033 restraints weight = 21804.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.107474 restraints weight = 16209.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.7021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089   9970  Z= 0.171
  Angle     :  0.784  12.032  13514  Z= 0.423
  Chirality :  0.046   0.264   1563
  Planarity :  0.007   0.153   1689
  Dihedral  : 10.703 123.378   1464
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  9.11 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.49 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.24), residues: 1197
  helix: -0.13 (0.19), residues: 694
  sheet:  0.61 (0.49), residues: 102
  loop : -2.02 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  92 
 HIS   0.030   0.002   HIS B 196 
 PHE   0.041   0.003   PHE B  66 
 TYR   0.024   0.002   TYR B  98 
 ARG   0.011   0.001   ARG B 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05577 (  595)
  hydrogen bonds       : angle       6.04341 ( 1728)
  covalent geometry    : bond        0.00353 ( 9970)
  covalent geometry    : angle       0.78359 (13514)

*********************** 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
  343 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 340
  time to evaluate  : 1.007 
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: 0.5733 (m-80) cc_final: 0.5487 (m-80)
REVERT: A   54 GLN cc_start: 0.9420 (mt0) cc_final: 0.9084 (mm-40)
REVERT: A   76 MET cc_start: 0.9328 (ptt) cc_final: 0.8569 (tmm)
REVERT: A   77 LEU cc_start: 0.9058 (mt) cc_final: 0.8633 (mt)
REVERT: A   79 LEU cc_start: 0.9007 (mm) cc_final: 0.8757 (mm)
REVERT: A   80 HIS cc_start: 0.7772 (m170) cc_final: 0.7179 (m170)
REVERT: A  109 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8449 (ttpp)
REVERT: A  116 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7667 (mmp80)
REVERT: A  153 PHE cc_start: 0.9162 (t80) cc_final: 0.8813 (t80)
REVERT: A  174 ARG cc_start: 0.9230 (mtp180) cc_final: 0.8975 (mtp180)
REVERT: A  253 HIS cc_start: 0.8080 (m90) cc_final: 0.7617 (m90)
REVERT: A  327 HIS cc_start: 0.7361 (m-70) cc_final: 0.5771 (m-70)
REVERT: A  359 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.9012 (pm20)
REVERT: A  373 LYS cc_start: 0.9661 (tmmt) cc_final: 0.9150 (mttt)
REVERT: A  376 LEU cc_start: 0.9714 (mm) cc_final: 0.9368 (mm)
REVERT: A  380 HIS cc_start: 0.9369 (m-70) cc_final: 0.8896 (m-70)
REVERT: B   19 MET cc_start: 0.8196 (pmm) cc_final: 0.7428 (pmm)
REVERT: B   54 GLN cc_start: 0.9587 (pp30) cc_final: 0.9227 (pp30)
REVERT: B   55 LEU cc_start: 0.9180 (mt) cc_final: 0.8788 (mt)
REVERT: B   74 LEU cc_start: 0.9390 (mt) cc_final: 0.9166 (mt)
REVERT: B   78 CYS cc_start: 0.8807 (p) cc_final: 0.8560 (p)
REVERT: B  187 TYR cc_start: 0.7217 (t80) cc_final: 0.6899 (t80)
REVERT: B  198 MET cc_start: 0.8472 (mmt) cc_final: 0.8097 (mmt)
REVERT: B  307 ASN cc_start: 0.8313 (m110) cc_final: 0.7863 (t0)
REVERT: B  354 LEU cc_start: 0.9579 (mm) cc_final: 0.9251 (mm)
REVERT: B  363 LEU cc_start: 0.9345 (mt) cc_final: 0.8835 (mt)
REVERT: B  366 LEU cc_start: 0.7526 (tp) cc_final: 0.6743 (tt)
REVERT: B  376 LEU cc_start: 0.9713 (mt) cc_final: 0.9303 (mt)
REVERT: B  377 MET cc_start: 0.9585 (ttm) cc_final: 0.9367 (ttm)
REVERT: B  380 HIS cc_start: 0.9040 (m90) cc_final: 0.8365 (m90)
REVERT: B  382 LYS cc_start: 0.9768 (mmmm) cc_final: 0.9453 (mmmm)
REVERT: B  386 ILE cc_start: 0.9512 (tp) cc_final: 0.9310 (tp)
REVERT: B  394 MET cc_start: 0.9435 (ttm) cc_final: 0.9206 (tpp)
REVERT: C   42 TRP cc_start: 0.8417 (t-100) cc_final: 0.7955 (t-100)
REVERT: C   88 GLU cc_start: 0.8725 (tp30) cc_final: 0.8490 (tp30)
REVERT: C   91 LEU cc_start: 0.9148 (tp) cc_final: 0.8772 (tp)
REVERT: C  149 MET cc_start: 0.6094 (ptt) cc_final: 0.5607 (ppp)
REVERT: C  159 LYS cc_start: 0.9064 (tmtt) cc_final: 0.8807 (ptpt)
REVERT: C  191 THR cc_start: 0.9253 (m) cc_final: 0.8901 (m)
REVERT: C  200 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8522 (mt-10)
REVERT: D   46 GLU cc_start: 0.8565 (tt0) cc_final: 0.8249 (tt0)
REVERT: D  124 ASP cc_start: 0.9634 (m-30) cc_final: 0.9389 (m-30)
REVERT: D  126 LEU cc_start: 0.9697 (mt) cc_final: 0.9488 (mt)
REVERT: D  147 LEU cc_start: 0.8646 (mt) cc_final: 0.8293 (mt)
REVERT: D  149 MET cc_start: 0.8842 (mpp) cc_final: 0.8129 (mpp)
REVERT: D  157 ILE cc_start: 0.9245 (mt) cc_final: 0.9037 (mt)
REVERT: D  167 LEU cc_start: 0.7038 (tp) cc_final: 0.6771 (tp)
REVERT: D  212 MET cc_start: 0.3650 (ttt) cc_final: 0.3130 (ptt)
  outliers start: 3
  outliers final: 0
  residues processed: 342
  average time/residue: 0.2221
  time to fit residues: 104.5871
Evaluate side-chains
  281 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 280
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0670
   chunk 2 optimal weight:    0.0870
   chunk 96 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 129 ASN
** 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 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 = 0.4018 r_free = 0.4018 target = 0.130383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.104762 restraints weight = 31873.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.108145 restraints weight = 21605.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.110672 restraints weight = 15913.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.7408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093   9970  Z= 0.165
  Angle     :  0.826  11.387  13514  Z= 0.435
  Chirality :  0.047   0.266   1563
  Planarity :  0.006   0.151   1689
  Dihedral  : 10.583 123.162   1464
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.19 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.24), residues: 1197
  helix: -0.22 (0.19), residues: 696
  sheet:  0.78 (0.50), residues: 98
  loop : -2.06 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  92 
 HIS   0.020   0.001   HIS B 196 
 PHE   0.032   0.002   PHE A 201 
 TYR   0.023   0.002   TYR B  98 
 ARG   0.007   0.001   ARG C  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05322 (  595)
  hydrogen bonds       : angle       6.02948 ( 1728)
  covalent geometry    : bond        0.00339 ( 9970)
  covalent geometry    : angle       0.82646 (13514)

*********************** 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
  346 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 346
  time to evaluate  : 1.080 
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: A   54 GLN cc_start: 0.9401 (mt0) cc_final: 0.9074 (mm-40)
REVERT: A   76 MET cc_start: 0.9276 (ptt) cc_final: 0.8521 (tmm)
REVERT: A   77 LEU cc_start: 0.9081 (mt) cc_final: 0.8664 (mt)
REVERT: A   79 LEU cc_start: 0.8977 (mm) cc_final: 0.8743 (mm)
REVERT: A   80 HIS cc_start: 0.7576 (m170) cc_final: 0.7072 (m170)
REVERT: A  109 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8419 (ttpp)
REVERT: A  153 PHE cc_start: 0.9115 (t80) cc_final: 0.8813 (t80)
REVERT: A  209 LEU cc_start: 0.9414 (pt) cc_final: 0.9181 (pp)
REVERT: A  210 ILE cc_start: 0.8932 (mm) cc_final: 0.8702 (mm)
REVERT: A  213 LEU cc_start: 0.8859 (tt) cc_final: 0.8607 (tt)
REVERT: A  253 HIS cc_start: 0.7967 (m90) cc_final: 0.7518 (m90)
REVERT: A  327 HIS cc_start: 0.7362 (m-70) cc_final: 0.5760 (m-70)
REVERT: A  373 LYS cc_start: 0.9625 (tmmt) cc_final: 0.9123 (mttt)
REVERT: A  377 MET cc_start: 0.9140 (tmm) cc_final: 0.8862 (tmm)
REVERT: B   19 MET cc_start: 0.8304 (pmm) cc_final: 0.7144 (pmm)
REVERT: B   54 GLN cc_start: 0.9580 (pp30) cc_final: 0.9172 (pp30)
REVERT: B   55 LEU cc_start: 0.9106 (mt) cc_final: 0.8684 (mt)
REVERT: B   66 PHE cc_start: 0.7018 (t80) cc_final: 0.6716 (t80)
REVERT: B   78 CYS cc_start: 0.8894 (p) cc_final: 0.8668 (p)
REVERT: B   88 LYS cc_start: 0.9467 (tttt) cc_final: 0.9066 (tptp)
REVERT: B  179 HIS cc_start: 0.8639 (m-70) cc_final: 0.8355 (m-70)
REVERT: B  187 TYR cc_start: 0.6979 (t80) cc_final: 0.6753 (t80)
REVERT: B  197 MET cc_start: 0.7328 (mpp) cc_final: 0.6711 (ptp)
REVERT: B  198 MET cc_start: 0.8141 (mmt) cc_final: 0.7840 (mmt)
REVERT: B  201 PHE cc_start: 0.8581 (m-10) cc_final: 0.7667 (m-80)
REVERT: B  298 ARG cc_start: 0.8152 (tpm170) cc_final: 0.7489 (tpp-160)
REVERT: B  344 ARG cc_start: 0.9361 (ttt-90) cc_final: 0.8914 (mmm160)
REVERT: B  354 LEU cc_start: 0.9568 (mm) cc_final: 0.9368 (mm)
REVERT: B  355 GLN cc_start: 0.9531 (mt0) cc_final: 0.9084 (mp10)
REVERT: B  363 LEU cc_start: 0.9373 (mt) cc_final: 0.8840 (mt)
REVERT: B  366 LEU cc_start: 0.7494 (tp) cc_final: 0.6717 (tt)
REVERT: B  376 LEU cc_start: 0.9719 (mt) cc_final: 0.9262 (mt)
REVERT: B  377 MET cc_start: 0.9538 (ttm) cc_final: 0.9269 (ttm)
REVERT: B  380 HIS cc_start: 0.9033 (m90) cc_final: 0.8443 (m90)
REVERT: B  382 LYS cc_start: 0.9770 (mmmm) cc_final: 0.9438 (mmmm)
REVERT: B  386 ILE cc_start: 0.9537 (tp) cc_final: 0.9332 (tp)
REVERT: B  400 GLU cc_start: 0.9425 (mm-30) cc_final: 0.9155 (mm-30)
REVERT: C   42 TRP cc_start: 0.8235 (t-100) cc_final: 0.7915 (t-100)
REVERT: C   72 THR cc_start: 0.8799 (m) cc_final: 0.8554 (p)
REVERT: C   88 GLU cc_start: 0.8939 (tp30) cc_final: 0.8621 (tp30)
REVERT: C   91 LEU cc_start: 0.9115 (tp) cc_final: 0.8643 (tp)
REVERT: C  149 MET cc_start: 0.6184 (ptt) cc_final: 0.5749 (ppp)
REVERT: C  163 LYS cc_start: 0.7150 (tttt) cc_final: 0.6639 (pttt)
REVERT: D  109 GLN cc_start: 0.9099 (mp10) cc_final: 0.8807 (mp10)
REVERT: D  124 ASP cc_start: 0.9653 (m-30) cc_final: 0.9436 (m-30)
REVERT: D  147 LEU cc_start: 0.8604 (mt) cc_final: 0.8246 (mt)
REVERT: D  149 MET cc_start: 0.8738 (mpp) cc_final: 0.7938 (mpp)
REVERT: D  167 LEU cc_start: 0.6625 (tp) cc_final: 0.6262 (tp)
REVERT: D  212 MET cc_start: 0.3757 (ttt) cc_final: 0.3166 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 346
  average time/residue: 0.2365
  time to fit residues: 114.4975
Evaluate side-chains
  282 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 27 optimal weight:    0.1980
   chunk 37 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 129 ASN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN
** D  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 105 GLN
D 186 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.129561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.104052 restraints weight = 32595.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.107422 restraints weight = 21957.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.109895 restraints weight = 16123.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.7628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   9970  Z= 0.169
  Angle     :  0.820  12.448  13514  Z= 0.438
  Chirality :  0.046   0.263   1563
  Planarity :  0.006   0.150   1689
  Dihedral  : 10.539 121.720   1464
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  7.85 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.24), residues: 1197
  helix: -0.25 (0.19), residues: 698
  sheet:  0.68 (0.51), residues: 100
  loop : -2.16 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  42 
 HIS   0.008   0.001   HIS C  58 
 PHE   0.034   0.003   PHE B 296 
 TYR   0.023   0.002   TYR B  98 
 ARG   0.009   0.001   ARG B 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05211 (  595)
  hydrogen bonds       : angle       6.07027 ( 1728)
  covalent geometry    : bond        0.00354 ( 9970)
  covalent geometry    : angle       0.82001 (13514)

*********************** 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
  336 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 336
  time to evaluate  : 1.026 
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   44 TYR cc_start: 0.5447 (m-80) cc_final: 0.5116 (m-80)
REVERT: A   76 MET cc_start: 0.9265 (ptt) cc_final: 0.8443 (tmm)
REVERT: A   77 LEU cc_start: 0.9055 (mt) cc_final: 0.8611 (mt)
REVERT: A   80 HIS cc_start: 0.7663 (m170) cc_final: 0.7112 (m170)
REVERT: A  109 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8409 (ttpp)
REVERT: A  118 GLU cc_start: 0.8908 (pt0) cc_final: 0.8567 (pt0)
REVERT: A  132 ARG cc_start: 0.8450 (ptt-90) cc_final: 0.8074 (ptt-90)
REVERT: A  153 PHE cc_start: 0.9143 (t80) cc_final: 0.8815 (t80)
REVERT: A  253 HIS cc_start: 0.8160 (m90) cc_final: 0.7559 (m90)
REVERT: A  327 HIS cc_start: 0.7502 (m-70) cc_final: 0.5838 (m-70)
REVERT: A  351 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8819 (tm-30)
REVERT: A  370 ASP cc_start: 0.9045 (p0) cc_final: 0.8435 (p0)
REVERT: A  373 LYS cc_start: 0.9623 (tmmt) cc_final: 0.9156 (mttt)
REVERT: A  377 MET cc_start: 0.9105 (tmm) cc_final: 0.8818 (tmm)
REVERT: B   20 ASP cc_start: 0.8217 (m-30) cc_final: 0.7473 (m-30)
REVERT: B   66 PHE cc_start: 0.7229 (t80) cc_final: 0.6964 (t80)
REVERT: B   78 CYS cc_start: 0.8875 (p) cc_final: 0.8633 (p)
REVERT: B   88 LYS cc_start: 0.9464 (tttt) cc_final: 0.9093 (tptp)
REVERT: B  179 HIS cc_start: 0.8631 (m-70) cc_final: 0.8376 (m-70)
REVERT: B  197 MET cc_start: 0.7298 (mpp) cc_final: 0.6985 (ptp)
REVERT: B  198 MET cc_start: 0.8247 (mmt) cc_final: 0.7877 (mmt)
REVERT: B  298 ARG cc_start: 0.8177 (tpm170) cc_final: 0.7406 (tpp-160)
REVERT: B  351 GLU cc_start: 0.8984 (tp30) cc_final: 0.8423 (tm-30)
REVERT: B  363 LEU cc_start: 0.9344 (mt) cc_final: 0.8856 (mt)
REVERT: B  366 LEU cc_start: 0.7596 (tp) cc_final: 0.6808 (tt)
REVERT: B  376 LEU cc_start: 0.9722 (mt) cc_final: 0.9302 (mt)
REVERT: B  377 MET cc_start: 0.9602 (ttm) cc_final: 0.9359 (ttm)
REVERT: B  380 HIS cc_start: 0.9050 (m90) cc_final: 0.8571 (m-70)
REVERT: B  382 LYS cc_start: 0.9767 (mmmm) cc_final: 0.9493 (mmmm)
REVERT: B  394 MET cc_start: 0.9634 (tpp) cc_final: 0.9313 (tpp)
REVERT: C   42 TRP cc_start: 0.8413 (t-100) cc_final: 0.8038 (t-100)
REVERT: C   88 GLU cc_start: 0.8962 (tp30) cc_final: 0.8631 (tp30)
REVERT: C   91 LEU cc_start: 0.9122 (tp) cc_final: 0.8655 (tp)
REVERT: C  149 MET cc_start: 0.6285 (ptt) cc_final: 0.6038 (ptt)
REVERT: C  159 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8752 (ttpp)
REVERT: C  160 PHE cc_start: 0.8727 (t80) cc_final: 0.8273 (t80)
REVERT: C  163 LYS cc_start: 0.7299 (tttt) cc_final: 0.6783 (pttt)
REVERT: C  222 LEU cc_start: 0.8971 (tt) cc_final: 0.8713 (tt)
REVERT: D   41 TYR cc_start: 0.7431 (t80) cc_final: 0.6336 (t80)
REVERT: D   46 GLU cc_start: 0.8876 (tt0) cc_final: 0.7933 (mp0)
REVERT: D  124 ASP cc_start: 0.9668 (m-30) cc_final: 0.9362 (m-30)
REVERT: D  147 LEU cc_start: 0.8587 (mt) cc_final: 0.8301 (mt)
REVERT: D  209 MET cc_start: 0.1650 (ppp) cc_final: -0.0380 (mmt)
REVERT: D  212 MET cc_start: 0.3708 (ttt) cc_final: 0.3111 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 336
  average time/residue: 0.2273
  time to fit residues: 106.0121
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  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 108 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN
** D  58 HIS ** 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 = 0.4008 r_free = 0.4008 target = 0.130507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.105601 restraints weight = 31264.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.109067 restraints weight = 20657.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.111644 restraints weight = 14906.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.7935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   9970  Z= 0.169
  Angle     :  0.832  11.588  13514  Z= 0.442
  Chirality :  0.047   0.287   1563
  Planarity :  0.006   0.149   1689
  Dihedral  : 10.490 120.255   1464
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.10 %
    Favored  : 91.48 %
  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 : 6.06 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.24), residues: 1197
  helix: -0.30 (0.19), residues: 702
  sheet:  0.72 (0.50), residues: 103
  loop : -2.22 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  42 
 HIS   0.017   0.001   HIS B 196 
 PHE   0.027   0.002   PHE B 157 
 TYR   0.022   0.002   TYR B  98 
 ARG   0.009   0.001   ARG D 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05193 (  595)
  hydrogen bonds       : angle       6.09921 ( 1728)
  covalent geometry    : bond        0.00355 ( 9970)
  covalent geometry    : angle       0.83225 (13514)

*********************** 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
  348 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 348
  time to evaluate  : 1.027 
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: A   44 TYR cc_start: 0.5414 (m-80) cc_final: 0.5170 (m-80)
REVERT: A   54 GLN cc_start: 0.9414 (mt0) cc_final: 0.9085 (mm-40)
REVERT: A   76 MET cc_start: 0.9276 (ptt) cc_final: 0.8503 (tmm)
REVERT: A   77 LEU cc_start: 0.9003 (mt) cc_final: 0.8546 (mt)
REVERT: A   80 HIS cc_start: 0.7723 (m170) cc_final: 0.7199 (m170)
REVERT: A  109 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8369 (ttpp)
REVERT: A  118 GLU cc_start: 0.8909 (pt0) cc_final: 0.8468 (pt0)
REVERT: A  153 PHE cc_start: 0.9133 (t80) cc_final: 0.8243 (t80)
REVERT: A  179 HIS cc_start: 0.8499 (m-70) cc_final: 0.8259 (m-70)
REVERT: A  200 ILE cc_start: 0.9470 (tt) cc_final: 0.9085 (tt)
REVERT: A  210 ILE cc_start: 0.8996 (mm) cc_final: 0.8758 (mm)
REVERT: A  244 LEU cc_start: 0.5169 (mt) cc_final: 0.3599 (mm)
REVERT: A  253 HIS cc_start: 0.8189 (m90) cc_final: 0.7588 (m90)
REVERT: A  327 HIS cc_start: 0.7461 (m-70) cc_final: 0.5819 (m-70)
REVERT: B   78 CYS cc_start: 0.8848 (p) cc_final: 0.8597 (p)
REVERT: B   88 LYS cc_start: 0.9454 (tttt) cc_final: 0.9062 (tptp)
REVERT: B  179 HIS cc_start: 0.8570 (m-70) cc_final: 0.8335 (m-70)
REVERT: B  198 MET cc_start: 0.8038 (mmt) cc_final: 0.7654 (mmt)
REVERT: B  298 ARG cc_start: 0.8205 (tpm170) cc_final: 0.7372 (tpp-160)
REVERT: B  351 GLU cc_start: 0.8952 (tp30) cc_final: 0.8596 (tp30)
REVERT: B  355 GLN cc_start: 0.9419 (mt0) cc_final: 0.8845 (mt0)
REVERT: B  363 LEU cc_start: 0.9345 (mt) cc_final: 0.8866 (mt)
REVERT: B  366 LEU cc_start: 0.7641 (tp) cc_final: 0.7051 (tt)
REVERT: B  376 LEU cc_start: 0.9712 (mt) cc_final: 0.9268 (mt)
REVERT: B  380 HIS cc_start: 0.8924 (m90) cc_final: 0.8355 (m-70)
REVERT: B  382 LYS cc_start: 0.9767 (mmmm) cc_final: 0.9497 (mmmm)
REVERT: B  394 MET cc_start: 0.9614 (tpp) cc_final: 0.9320 (tpp)
REVERT: B  400 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9186 (mm-30)
REVERT: C   42 TRP cc_start: 0.8372 (t-100) cc_final: 0.7975 (t-100)
REVERT: C   88 GLU cc_start: 0.8973 (tp30) cc_final: 0.8639 (tp30)
REVERT: C   91 LEU cc_start: 0.9072 (tp) cc_final: 0.8687 (tp)
REVERT: C  149 MET cc_start: 0.6281 (ptt) cc_final: 0.6011 (ptt)
REVERT: C  159 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8779 (ttpp)
REVERT: C  163 LYS cc_start: 0.7421 (tttt) cc_final: 0.6903 (pttt)
REVERT: D  113 GLU cc_start: 0.7946 (tp30) cc_final: 0.7686 (tp30)
REVERT: D  115 LEU cc_start: 0.8920 (mp) cc_final: 0.8145 (tt)
REVERT: D  123 SER cc_start: 0.9427 (m) cc_final: 0.9180 (m)
REVERT: D  147 LEU cc_start: 0.8682 (mt) cc_final: 0.8400 (mt)
REVERT: D  149 MET cc_start: 0.9033 (mpp) cc_final: 0.8210 (mpp)
REVERT: D  209 MET cc_start: 0.1690 (ppp) cc_final: -0.0321 (mmt)
REVERT: D  212 MET cc_start: 0.3534 (ttt) cc_final: 0.2914 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 348
  average time/residue: 0.2052
  time to fit residues: 99.9771
Evaluate side-chains
  285 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 106 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 179 HIS
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN
** D  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.127869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.102408 restraints weight = 32395.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.105685 restraints weight = 21915.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.108014 restraints weight = 16133.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.8040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   9970  Z= 0.181
  Angle     :  0.838  16.731  13514  Z= 0.447
  Chirality :  0.047   0.279   1563
  Planarity :  0.007   0.151   1689
  Dihedral  : 10.543 119.561   1464
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  8.86 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.24), residues: 1197
  helix: -0.26 (0.19), residues: 692
  sheet:  0.69 (0.52), residues: 99
  loop : -2.15 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  42 
 HIS   0.017   0.002   HIS B 196 
 PHE   0.036   0.003   PHE B  66 
 TYR   0.030   0.002   TYR B 357 
 ARG   0.007   0.001   ARG D 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05397 (  595)
  hydrogen bonds       : angle       6.20273 ( 1728)
  covalent geometry    : bond        0.00382 ( 9970)
  covalent geometry    : angle       0.83778 (13514)

********************** 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
  337 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 1.091 
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: A   44 TYR cc_start: 0.5368 (m-80) cc_final: 0.5074 (m-80)
REVERT: A   76 MET cc_start: 0.9323 (ptt) cc_final: 0.8594 (tmm)
REVERT: A   77 LEU cc_start: 0.9116 (mt) cc_final: 0.8721 (mt)
REVERT: A   80 HIS cc_start: 0.7761 (m170) cc_final: 0.7346 (m170)
REVERT: A  109 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8399 (ttpp)
REVERT: A  118 GLU cc_start: 0.8885 (pt0) cc_final: 0.8605 (pt0)
REVERT: A  130 ILE cc_start: 0.8829 (mp) cc_final: 0.8601 (mp)
REVERT: A  153 PHE cc_start: 0.9111 (t80) cc_final: 0.8457 (t80)
REVERT: A  179 HIS cc_start: 0.8413 (m90) cc_final: 0.8197 (m-70)
REVERT: A  196 HIS cc_start: 0.7638 (t-170) cc_final: 0.7425 (t-170)
REVERT: A  217 GLN cc_start: 0.9440 (mp10) cc_final: 0.9209 (mp10)
REVERT: A  253 HIS cc_start: 0.8185 (m90) cc_final: 0.7542 (m90)
REVERT: A  327 HIS cc_start: 0.7521 (m-70) cc_final: 0.5834 (m-70)
REVERT: A  377 MET cc_start: 0.9124 (tmm) cc_final: 0.8884 (tmm)
REVERT: B   78 CYS cc_start: 0.8949 (p) cc_final: 0.8673 (p)
REVERT: B   88 LYS cc_start: 0.9479 (tttt) cc_final: 0.9083 (tptp)
REVERT: B  197 MET cc_start: 0.6918 (ptp) cc_final: 0.5388 (ptp)
REVERT: B  198 MET cc_start: 0.8381 (mmt) cc_final: 0.7706 (mmt)
REVERT: B  298 ARG cc_start: 0.8204 (tpm170) cc_final: 0.7457 (tpp-160)
REVERT: B  351 GLU cc_start: 0.9044 (tp30) cc_final: 0.8672 (tp30)
REVERT: B  355 GLN cc_start: 0.9427 (mt0) cc_final: 0.8866 (mt0)
REVERT: B  363 LEU cc_start: 0.9389 (mt) cc_final: 0.8921 (mt)
REVERT: B  366 LEU cc_start: 0.7740 (tp) cc_final: 0.6937 (tt)
REVERT: B  376 LEU cc_start: 0.9697 (mt) cc_final: 0.9243 (mt)
REVERT: B  380 HIS cc_start: 0.8965 (m90) cc_final: 0.8439 (m-70)
REVERT: B  382 LYS cc_start: 0.9773 (mmmm) cc_final: 0.9520 (mmmm)
REVERT: B  394 MET cc_start: 0.9687 (tpp) cc_final: 0.9350 (tpp)
REVERT: B  400 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9202 (mm-30)
REVERT: C   42 TRP cc_start: 0.8509 (t-100) cc_final: 0.8100 (t-100)
REVERT: C   88 GLU cc_start: 0.8937 (tp30) cc_final: 0.8632 (tp30)
REVERT: C   91 LEU cc_start: 0.9236 (tp) cc_final: 0.8747 (tp)
REVERT: C  149 MET cc_start: 0.6493 (ptt) cc_final: 0.6180 (ptt)
REVERT: C  159 LYS cc_start: 0.9090 (tmtt) cc_final: 0.8716 (ttpp)
REVERT: C  163 LYS cc_start: 0.7444 (tttt) cc_final: 0.6929 (pttt)
REVERT: D   95 ARG cc_start: 0.7973 (ptm-80) cc_final: 0.7728 (ptm-80)
REVERT: D  113 GLU cc_start: 0.8257 (tp30) cc_final: 0.7969 (tp30)
REVERT: D  115 LEU cc_start: 0.8977 (mp) cc_final: 0.8301 (tt)
REVERT: D  123 SER cc_start: 0.9464 (m) cc_final: 0.9206 (m)
REVERT: D  147 LEU cc_start: 0.8533 (mt) cc_final: 0.8279 (mt)
REVERT: D  149 MET cc_start: 0.8953 (mpp) cc_final: 0.8105 (mpp)
REVERT: D  209 MET cc_start: 0.1621 (ppp) cc_final: -0.0483 (mmt)
REVERT: D  212 MET cc_start: 0.3502 (ttt) cc_final: 0.2867 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.2103
  time to fit residues: 99.8488
Evaluate side-chains
  282 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 117 optimal weight:    8.9990
   chunk 59 optimal weight:    0.0370
   overall best weight:    1.0064

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN
** D  58 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 = 0.4010 r_free = 0.4010 target = 0.129915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.104307 restraints weight = 31672.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.107625 restraints weight = 21481.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.110107 restraints weight = 15850.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.8260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   9970  Z= 0.171
  Angle     :  0.847  14.318  13514  Z= 0.449
  Chirality :  0.047   0.281   1563
  Planarity :  0.006   0.149   1689
  Dihedral  : 10.458 118.633   1464
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  8.94 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.24), residues: 1197
  helix: -0.30 (0.19), residues: 692
  sheet:  0.78 (0.54), residues: 97
  loop : -2.20 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 191 
 HIS   0.010   0.001   HIS C  58 
 PHE   0.035   0.002   PHE B  66 
 TYR   0.029   0.002   TYR B 357 
 ARG   0.006   0.001   ARG D 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05312 (  595)
  hydrogen bonds       : angle       6.13076 ( 1728)
  covalent geometry    : bond        0.00363 ( 9970)
  covalent geometry    : angle       0.84715 (13514)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3807.35 seconds
wall clock time: 68 minutes 8.96 seconds (4088.96 seconds total)