Starting phenix.real_space_refine
on Wed Sep 17 16:47:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9j_39081/09_2025/8y9j_39081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9j_39081/09_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_39081/09_2025/8y9j_39081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9j_39081/09_2025/8y9j_39081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9j_39081/09_2025/8y9j_39081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9j_39081/09_2025/8y9j_39081.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      41      5.16       5
     C    6190      2.51       5
     N    1704      2.21       5
     O    1823      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9770
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3071
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 8, 'TRANS': 381}
    Chain: "B"
      Number of atoms: 3066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3066
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 8, 'TRANS': 380}
    Chain: "C"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1764
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 9, 'TRANS': 212}
    Chain: "D"
      Number of atoms: 1629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1629
          Classifications: {'peptide': 204}
          Link IDs: {'PTRANS': 8, 'TRANS': 195}
    Chain: "K"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 240
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
  Time building chain proxies: 2.32, per 1000 atoms: 0.24
  Number of scatterers: 9770
  At special positions: 0
  Unit cell: (116.325, 120.037, 106.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P      12     15.00
     O    1823      8.00
     N    1704      7.00
     C    6190      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 305.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 29
    Processing helix  chain 'A' and resid 48 through 64
      removed outlier: 3.952A  pdb=" N   ILE A  52 " --> pdb=" O   ASN A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 84
      removed outlier: 3.808A  pdb=" N   GLN A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 91
      removed outlier: 4.239A  pdb=" N   LEU A  89 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 124 through 137
      removed outlier: 4.138A  pdb=" N   ASN A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ILE A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 157
      removed outlier: 3.852A  pdb=" N   PHE A 157 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 183
      removed outlier: 4.021A  pdb=" N   LEU A 169 " --> pdb=" O   GLU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 221
      removed outlier: 4.249A  pdb=" N   GLN A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   HIS A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   MET A 198 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG A 202 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG A 205 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   THR A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   LEU A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ILE A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
      removed outlier: 3.821A  pdb=" N   ALA A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 290
      removed outlier: 3.714A  pdb=" N   GLU A 276 " --> pdb=" O   LYS A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.648A  pdb=" N   ARG A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU A 299 " --> pdb=" O   PRO A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 308
      removed outlier: 3.665A  pdb=" N   ASN A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 329
    Processing helix  chain 'A' and resid 330 through 335
      removed outlier: 3.594A  pdb=" N   GLY A 333 " --> pdb=" O   THR A 330 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ASN A 335 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 366
      removed outlier: 3.523A  pdb=" N   LEU A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASP A 364 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 408
    Processing helix  chain 'B' and resid 21 through 28
      removed outlier: 4.120A  pdb=" N   LEU B  25 " --> pdb=" O   TYR B  21 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY B  28 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 64
      removed outlier: 3.827A  pdb=" N   VAL B  64 " --> pdb=" O   PHE B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 83
    Processing helix  chain 'B' and resid 85 through 93
      removed outlier: 4.215A  pdb=" N   LEU B  89 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 115 through 121
    Processing helix  chain 'B' and resid 124 through 137
      removed outlier: 3.790A  pdb=" N   ASN B 129 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG B 132 " --> pdb=" O   LYS B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 157
      removed outlier: 4.017A  pdb=" N   PHE B 157 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 183
      removed outlier: 5.012A  pdb=" N   LYS B 166 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B 169 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 221
      removed outlier: 3.610A  pdb=" N   ARG B 202 " --> pdb=" O   MET B 198 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG B 205 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE B 208 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   LEU B 209 " --> pdb=" O   ARG B 205 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 240
    Processing helix  chain 'B' and resid 244 through 253
    Processing helix  chain 'B' and resid 270 through 291
      removed outlier: 3.875A  pdb=" N   LYS B 289 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   HIS B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
      Proline residue:  B 295  - end of helix
      No H-bonds generated for 'chain 'B' and resid 292 through 297'
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.933A  pdb=" N   ASN B 307 " --> pdb=" O   GLY B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 329
      removed outlier: 3.624A  pdb=" N   HIS B 327 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 335
      removed outlier: 3.587A  pdb=" N   ASN B 335 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 367
      removed outlier: 4.720A  pdb=" N   LEU B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLY B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 407
      removed outlier: 3.756A  pdb=" N   GLU B 372 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 27
      removed outlier: 3.545A  pdb=" N   GLY C  20 " --> pdb=" O   ASP C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 62
      removed outlier: 3.873A  pdb=" N   ALA C  55 " --> pdb=" O   HIS C  51 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU C  56 " --> pdb=" O   LYS C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 76
      removed outlier: 3.693A  pdb=" N   THR C  72 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 81
    Processing helix  chain 'C' and resid 88 through 105
    Processing helix  chain 'C' and resid 115 through 130
      removed outlier: 4.454A  pdb=" N   LEU C 119 " --> pdb=" O   LEU C 115 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR C 128 " --> pdb=" O   ASP C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 144
      removed outlier: 3.900A  pdb=" N   GLN C 144 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 166
      removed outlier: 3.567A  pdb=" N   SER C 151 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 210
      removed outlier: 3.832A  pdb=" N   SER C 207 " --> pdb=" O   PRO C 204 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA C 208 " --> pdb=" O   ASP C 205 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASN C 210 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 230
      removed outlier: 3.758A  pdb=" N   LYS C 228 " --> pdb=" O   GLU C 224 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   PHE C 230 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 61
      removed outlier: 3.763A  pdb=" N   LYS D  61 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 82
      removed outlier: 3.798A  pdb=" N   ASN D  74 " --> pdb=" O   SER D  70 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU D  75 " --> pdb=" O   MET D  71 " (cutoff:3.500A)
      Proline residue:  D  77  - end of helix
    Processing helix  chain 'D' and resid 90 through 106
    Processing helix  chain 'D' and resid 114 through 128
      removed outlier: 3.852A  pdb=" N   ALA D 118 " --> pdb=" O   PRO D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 144
    Processing helix  chain 'D' and resid 145 through 166
      removed outlier: 4.085A  pdb=" N   MET D 149 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA D 166 " --> pdb=" O   ASN D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 211
    Processing helix  chain 'D' and resid 223 through 230
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44
      removed outlier: 5.937A  pdb=" N   ARG A  39 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   GLU A 107 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE A  41 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   LYS A 109 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL A  43 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257
    Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 45
      removed outlier: 6.435A  pdb=" N   ARG B  39 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   GLU B 107 " --> pdb=" O   ARG B  39 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ILE B  41 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   LYS B 109 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   VAL B  43 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 258
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 34
    Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 87
      removed outlier: 6.882A  pdb=" N   THR C  86 " --> pdb=" O   PHE C 219 " (cutoff:3.500A)
      removed outlier: 8.794A  pdb=" N   LEU C 221 " --> pdb=" O   THR C  86 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE C 179 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 33
    Processing sheet with id=AA8, first strand: chain 'D' and resid 178 through 182

    595 hydrogen bonds defined for protein.
    1728 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2341
        1.33 -     1.45: 2064
        1.45 -     1.58: 5467
        1.58 -     1.70: 23
        1.70 -     1.82: 75
  Bond restraints: 9970
  Sorted by residual:
  bond pdb=" N   PRO D  77 "
       pdb=" CD  PRO D  77 "
    ideal  model  delta    sigma   weight residual
    1.473  1.419  0.054 1.40e-02 5.10e+03 1.51e+01
  bond pdb=" N   THR B 206 "
       pdb=" CA  THR B 206 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.25e-02 6.40e+03 1.14e+01
  bond pdb=" CA  GLN A  84 "
       pdb=" C   GLN A  84 "
    ideal  model  delta    sigma   weight residual
    1.524  1.568 -0.044 1.32e-02 5.74e+03 1.11e+01
  bond pdb=" C4'   U K   9 "
       pdb=" O4'   U K   9 "
    ideal  model  delta    sigma   weight residual
    1.454  1.406  0.048 1.50e-02 4.44e+03 1.04e+01
  bond pdb=" N   GLY D 215 "
       pdb=" CA  GLY D 215 "
    ideal  model  delta    sigma   weight residual
    1.434  1.472 -0.038 1.22e-02 6.72e+03 9.73e+00
  ... (remaining 9965 not shown)

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

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

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

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.540
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.160
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.49 (0.20), residues: 1197
  helix: -1.13 (0.16), residues: 663
  sheet:  0.89 (0.50), residues: 88
  loop : -2.94 (0.26), residues: 446

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

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

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 443
  time to evaluate  : 0.419 
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: 0.1000
  time to fit residues: 62.7736
Evaluate side-chains
  338 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 326
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   overall best weight:    2.5788

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

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 225 HIS
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 GLN
B 175 GLN
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
B 228 ASN
B 306 ASN
** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 162 ASN
** C 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS
D 202 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.121570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.096784 restraints weight = 31372.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.100056 restraints weight = 20875.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.102403 restraints weight = 15218.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.104320 restraints weight = 11875.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.105659 restraints weight = 9632.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.103   9970  Z= 0.233
  Angle     :  0.953  13.655  13514  Z= 0.515
  Chirality :  0.050   0.245   1563
  Planarity :  0.008   0.169   1689
  Dihedral  : 12.783 137.586   1464
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  8.94 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.98 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.86 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.23), residues: 1197
  helix: -0.08 (0.18), residues: 679
  sheet:  0.42 (0.45), residues: 115
  loop : -2.75 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 132 
 TYR   0.047   0.003   TYR A  44 
 PHE   0.037   0.003   PHE B  66 
 TRP   0.029   0.003   TRP C  92 
 HIS   0.010   0.002   HIS C 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 9970)
  covalent geometry    : angle       0.95299 (13514)
  hydrogen bonds       : bond        0.07252 (  595)
  hydrogen bonds       : angle       6.84403 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 363
  time to evaluate  : 0.372 
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   79 LEU cc_start: 0.9049 (mm) cc_final: 0.8826 (mm)
REVERT: A   98 TYR cc_start: 0.7533 (t80) cc_final: 0.7292 (t80)
REVERT: A  110 LYS cc_start: 0.9357 (tptm) cc_final: 0.8936 (tppp)
REVERT: A  116 ARG cc_start: 0.8316 (mmt-90) cc_final: 0.7759 (mmp80)
REVERT: A  153 PHE cc_start: 0.9126 (t80) cc_final: 0.8565 (t80)
REVERT: A  179 HIS cc_start: 0.8475 (m-70) cc_final: 0.8113 (m-70)
REVERT: A  201 PHE cc_start: 0.8713 (m-80) cc_final: 0.8486 (m-80)
REVERT: A  213 LEU cc_start: 0.9500 (tt) cc_final: 0.9162 (tt)
REVERT: A  308 LEU cc_start: 0.8666 (mm) cc_final: 0.8418 (mm)
REVERT: A  359 GLU cc_start: 0.9235 (tt0) cc_final: 0.8904 (tt0)
REVERT: A  362 GLU cc_start: 0.9527 (OUTLIER) cc_final: 0.9223 (pp20)
REVERT: A  376 LEU cc_start: 0.9742 (mm) cc_final: 0.9344 (mm)
REVERT: A  380 HIS cc_start: 0.9376 (m-70) cc_final: 0.8770 (m-70)
REVERT: B   19 MET cc_start: 0.7686 (pmm) cc_final: 0.6884 (pmm)
REVERT: B   39 ARG cc_start: 0.8802 (mmt-90) cc_final: 0.8456 (mmt180)
REVERT: B   76 MET cc_start: 0.9361 (ptp) cc_final: 0.9005 (ptt)
REVERT: B   78 CYS cc_start: 0.8505 (p) cc_final: 0.8266 (p)
REVERT: B  109 LYS cc_start: 0.8948 (mttt) cc_final: 0.8706 (mtpt)
REVERT: B  208 PHE cc_start: 0.8686 (p90) cc_final: 0.8365 (p90)
REVERT: B  284 LEU cc_start: 0.9571 (mm) cc_final: 0.9076 (pp)
REVERT: B  327 HIS cc_start: 0.7609 (m-70) cc_final: 0.7368 (m170)
REVERT: B  376 LEU cc_start: 0.9705 (mt) cc_final: 0.9298 (mt)
REVERT: B  380 HIS cc_start: 0.9302 (m90) cc_final: 0.8782 (m90)
REVERT: C   42 TRP cc_start: 0.8521 (t60) cc_final: 0.7803 (t60)
REVERT: C   52 LYS cc_start: 0.6826 (mttm) cc_final: 0.6567 (mmmt)
REVERT: C  159 LYS cc_start: 0.8241 (mttt) cc_final: 0.7870 (tptp)
REVERT: C  160 PHE cc_start: 0.8898 (t80) cc_final: 0.8597 (t80)
REVERT: C  181 ILE cc_start: 0.8596 (mm) cc_final: 0.7580 (mp)
REVERT: C  191 THR cc_start: 0.9295 (m) cc_final: 0.8822 (p)
REVERT: C  198 LEU cc_start: 0.9199 (tp) cc_final: 0.8957 (tp)
REVERT: C  200 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8426 (mt-10)
REVERT: C  213 LYS cc_start: 0.8885 (tttt) cc_final: 0.8525 (tmtt)
REVERT: C  222 LEU cc_start: 0.9430 (pp) cc_final: 0.9174 (tp)
REVERT: D   87 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6713 (tp)
REVERT: D  109 GLN cc_start: 0.8874 (mt0) cc_final: 0.8510 (tt0)
REVERT: D  115 LEU cc_start: 0.9353 (mt) cc_final: 0.8728 (tt)
REVERT: D  119 LEU cc_start: 0.9686 (mt) cc_final: 0.9459 (mt)
REVERT: D  121 LEU cc_start: 0.9147 (mt) cc_final: 0.8672 (mt)
REVERT: D  124 ASP cc_start: 0.9578 (m-30) cc_final: 0.9071 (p0)
REVERT: D  134 PHE cc_start: 0.8724 (m-80) cc_final: 0.8482 (m-80)
REVERT: D  149 MET cc_start: 0.9383 (mpp) cc_final: 0.8863 (mpp)
REVERT: D  225 SER cc_start: 0.9161 (t) cc_final: 0.8826 (p)
  outliers start: 5
  outliers final: 0
  residues processed: 365
  average time/residue: 0.1023
  time to fit residues: 51.2702
Evaluate side-chains
  312 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 310
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0670
   chunk 32 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    2.8126

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
** A 192 GLN ** 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 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 GLN
** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.120452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.096668 restraints weight = 31683.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.099887 restraints weight = 20920.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.102284 restraints weight = 15188.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.104068 restraints weight = 11726.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.105414 restraints weight = 9511.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   9970  Z= 0.226
  Angle     :  0.891  12.721  13514  Z= 0.483
  Chirality :  0.048   0.244   1563
  Planarity :  0.007   0.162   1689
  Dihedral  : 11.927 130.650   1464
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 19.99
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.53 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.95 %
    Favored  : 94.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.60 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.23), residues: 1197
  helix: -0.08 (0.19), residues: 676
  sheet:  0.68 (0.45), residues: 107
  loop : -2.70 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 398 
 TYR   0.027   0.002   TYR B  98 
 PHE   0.047   0.003   PHE B  66 
 TRP   0.020   0.002   TRP C  42 
 HIS   0.030   0.002   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 9970)
  covalent geometry    : angle       0.89137 (13514)
  hydrogen bonds       : bond        0.06693 (  595)
  hydrogen bonds       : angle       6.64433 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 336
  time to evaluate  : 0.381 
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   51 GLU cc_start: 0.9358 (tt0) cc_final: 0.9115 (tt0)
REVERT: A   76 MET cc_start: 0.8956 (tmm) cc_final: 0.8441 (tmm)
REVERT: A   77 LEU cc_start: 0.9212 (mt) cc_final: 0.8556 (mt)
REVERT: A   79 LEU cc_start: 0.9161 (mm) cc_final: 0.8796 (mm)
REVERT: A  116 ARG cc_start: 0.8339 (mmt-90) cc_final: 0.7736 (mmp80)
REVERT: A  132 ARG cc_start: 0.8809 (mtm110) cc_final: 0.8304 (mtm180)
REVERT: A  179 HIS cc_start: 0.8411 (m-70) cc_final: 0.8050 (m-70)
REVERT: A  201 PHE cc_start: 0.8701 (m-80) cc_final: 0.8496 (m-80)
REVERT: A  204 MET cc_start: 0.8497 (tpp) cc_final: 0.7758 (tpp)
REVERT: A  209 LEU cc_start: 0.9470 (pt) cc_final: 0.9269 (pt)
REVERT: A  210 ILE cc_start: 0.9384 (mm) cc_final: 0.9180 (mm)
REVERT: A  211 LYS cc_start: 0.9280 (mttt) cc_final: 0.8559 (mttt)
REVERT: A  246 ILE cc_start: 0.9767 (mm) cc_final: 0.9490 (tp)
REVERT: A  372 GLU cc_start: 0.9102 (mp0) cc_final: 0.8859 (mp0)
REVERT: B   19 MET cc_start: 0.7824 (pmm) cc_final: 0.7250 (pmm)
REVERT: B   57 ILE cc_start: 0.9262 (tt) cc_final: 0.8829 (tt)
REVERT: B   74 LEU cc_start: 0.9387 (mt) cc_final: 0.9173 (mt)
REVERT: B   76 MET cc_start: 0.9378 (ptp) cc_final: 0.9108 (ptt)
REVERT: B   78 CYS cc_start: 0.8707 (p) cc_final: 0.8485 (p)
REVERT: B   88 LYS cc_start: 0.9500 (tttt) cc_final: 0.9135 (tptp)
REVERT: B  100 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8528 (tp30)
REVERT: B  109 LYS cc_start: 0.8861 (mttt) cc_final: 0.8649 (mtpt)
REVERT: B  198 MET cc_start: 0.8427 (mmt) cc_final: 0.8049 (mmt)
REVERT: B  351 GLU cc_start: 0.8973 (tp30) cc_final: 0.8714 (tp30)
REVERT: B  354 LEU cc_start: 0.9576 (mm) cc_final: 0.9331 (mm)
REVERT: B  355 GLN cc_start: 0.8856 (mt0) cc_final: 0.7901 (mt0)
REVERT: B  357 TYR cc_start: 0.8055 (t80) cc_final: 0.7796 (t80)
REVERT: B  363 LEU cc_start: 0.9358 (mt) cc_final: 0.8951 (mt)
REVERT: B  376 LEU cc_start: 0.9724 (mt) cc_final: 0.9239 (mt)
REVERT: B  377 MET cc_start: 0.9522 (ttm) cc_final: 0.9053 (mtp)
REVERT: B  380 HIS cc_start: 0.9132 (m90) cc_final: 0.8903 (m90)
REVERT: C   42 TRP cc_start: 0.8547 (t60) cc_final: 0.7993 (t60)
REVERT: C   52 LYS cc_start: 0.6502 (mttm) cc_final: 0.6171 (mmmt)
REVERT: C   76 PHE cc_start: 0.9148 (m-80) cc_final: 0.8921 (m-80)
REVERT: C  159 LYS cc_start: 0.8145 (mttt) cc_final: 0.7830 (tptp)
REVERT: C  160 PHE cc_start: 0.8832 (t80) cc_final: 0.8211 (t80)
REVERT: C  163 LYS cc_start: 0.7481 (tttt) cc_final: 0.6579 (pttt)
REVERT: C  191 THR cc_start: 0.9238 (m) cc_final: 0.8830 (p)
REVERT: C  198 LEU cc_start: 0.9258 (tp) cc_final: 0.8961 (tp)
REVERT: C  200 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: C  213 LYS cc_start: 0.8965 (tttt) cc_final: 0.8629 (tmtt)
REVERT: C  222 LEU cc_start: 0.9349 (pp) cc_final: 0.9063 (tt)
REVERT: D   31 VAL cc_start: 0.9052 (p) cc_final: 0.8683 (p)
REVERT: D  106 LEU cc_start: 0.9333 (mp) cc_final: 0.9113 (mt)
REVERT: D  115 LEU cc_start: 0.9335 (mt) cc_final: 0.8808 (tt)
REVERT: D  124 ASP cc_start: 0.9576 (m-30) cc_final: 0.9159 (m-30)
REVERT: D  149 MET cc_start: 0.9202 (mpp) cc_final: 0.8711 (mpp)
REVERT: D  165 ASP cc_start: 0.9221 (m-30) cc_final: 0.8933 (m-30)
REVERT: D  212 MET cc_start: 0.4931 (ttt) cc_final: 0.4485 (ptt)
REVERT: D  225 SER cc_start: 0.9227 (t) cc_final: 0.9022 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 337
  average time/residue: 0.0978
  time to fit residues: 45.7533
Evaluate side-chains
  277 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 276
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 46 optimal weight:    0.2980
   chunk 41 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 81 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
A 196 HIS
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 HIS
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 ASN
B 102 HIS
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  51 HIS
D 103 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.122890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.098721 restraints weight = 31864.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.101977 restraints weight = 21315.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.104389 restraints weight = 15537.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.106243 restraints weight = 12060.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.107562 restraints weight = 9774.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.5819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   9970  Z= 0.187
  Angle     :  0.809  12.336  13514  Z= 0.441
  Chirality :  0.046   0.255   1563
  Planarity :  0.007   0.159   1689
  Dihedral  : 11.288 127.004   1464
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 18.41
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  9.86 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.46 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.23), residues: 1197
  helix:  0.04 (0.19), residues: 686
  sheet:  0.77 (0.46), residues: 107
  loop : -2.68 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 398 
 TYR   0.026   0.002   TYR B  98 
 PHE   0.042   0.003   PHE B 157 
 TRP   0.043   0.003   TRP D  92 
 HIS   0.034   0.002   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9970)
  covalent geometry    : angle       0.80926 (13514)
  hydrogen bonds       : bond        0.05989 (  595)
  hydrogen bonds       : angle       6.39032 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 350
  time to evaluate  : 0.385 
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: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.8946 (tmm) cc_final: 0.8345 (tmm)
REVERT: A   77 LEU cc_start: 0.9223 (mt) cc_final: 0.8517 (mt)
REVERT: A   98 TYR cc_start: 0.7644 (t80) cc_final: 0.7255 (t80)
REVERT: A  116 ARG cc_start: 0.8303 (mmt-90) cc_final: 0.7991 (mmt-90)
REVERT: A  132 ARG cc_start: 0.8728 (mtm110) cc_final: 0.8417 (mtm180)
REVERT: A  153 PHE cc_start: 0.9182 (t80) cc_final: 0.8931 (t80)
REVERT: A  179 HIS cc_start: 0.8412 (m-70) cc_final: 0.7953 (m-70)
REVERT: A  201 PHE cc_start: 0.8491 (m-80) cc_final: 0.8239 (m-80)
REVERT: A  204 MET cc_start: 0.8386 (tpp) cc_final: 0.7494 (tpp)
REVERT: A  211 LYS cc_start: 0.9155 (mttt) cc_final: 0.8557 (mttt)
REVERT: A  246 ILE cc_start: 0.9746 (mm) cc_final: 0.9465 (tp)
REVERT: A  356 GLN cc_start: 0.9188 (mp10) cc_final: 0.8886 (mp10)
REVERT: A  372 GLU cc_start: 0.9087 (mp0) cc_final: 0.8825 (mp0)
REVERT: A  376 LEU cc_start: 0.9701 (mm) cc_final: 0.9258 (mm)
REVERT: A  377 MET cc_start: 0.9168 (tmm) cc_final: 0.8721 (tmm)
REVERT: A  380 HIS cc_start: 0.9311 (m-70) cc_final: 0.8591 (m90)
REVERT: A  398 ARG cc_start: 0.8707 (ttp-110) cc_final: 0.8452 (ttp-110)
REVERT: B   19 MET cc_start: 0.7892 (pmm) cc_final: 0.7316 (pmm)
REVERT: B   54 GLN cc_start: 0.9542 (pp30) cc_final: 0.9306 (pp30)
REVERT: B   55 LEU cc_start: 0.9213 (mt) cc_final: 0.8922 (mt)
REVERT: B   78 CYS cc_start: 0.8753 (p) cc_final: 0.8542 (p)
REVERT: B  198 MET cc_start: 0.8453 (mmt) cc_final: 0.8080 (mmt)
REVERT: B  255 LEU cc_start: 0.9540 (mm) cc_final: 0.9306 (pp)
REVERT: B  309 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8697 (mt-10)
REVERT: B  354 LEU cc_start: 0.9616 (mm) cc_final: 0.9321 (mm)
REVERT: B  363 LEU cc_start: 0.9329 (mt) cc_final: 0.8945 (mt)
REVERT: B  376 LEU cc_start: 0.9673 (mt) cc_final: 0.9173 (mt)
REVERT: B  380 HIS cc_start: 0.9096 (m90) cc_final: 0.8868 (m90)
REVERT: C   42 TRP cc_start: 0.8644 (t60) cc_final: 0.8098 (t60)
REVERT: C   52 LYS cc_start: 0.6580 (mttm) cc_final: 0.6319 (mmmt)
REVERT: C  159 LYS cc_start: 0.8022 (mttt) cc_final: 0.7741 (tptp)
REVERT: C  160 PHE cc_start: 0.8737 (t80) cc_final: 0.8165 (t80)
REVERT: C  163 LYS cc_start: 0.7334 (tttt) cc_final: 0.6528 (pttt)
REVERT: C  191 THR cc_start: 0.8975 (m) cc_final: 0.8526 (p)
REVERT: C  198 LEU cc_start: 0.9250 (tp) cc_final: 0.8894 (tp)
REVERT: C  200 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7988 (mt-10)
REVERT: C  213 LYS cc_start: 0.8944 (tttt) cc_final: 0.8583 (tmtt)
REVERT: C  222 LEU cc_start: 0.9396 (pp) cc_final: 0.9013 (tt)
REVERT: D   29 PHE cc_start: 0.8201 (m-10) cc_final: 0.7778 (m-80)
REVERT: D  115 LEU cc_start: 0.9229 (mt) cc_final: 0.8694 (tt)
REVERT: D  124 ASP cc_start: 0.9635 (m-30) cc_final: 0.9385 (m-30)
REVERT: D  149 MET cc_start: 0.9156 (mpp) cc_final: 0.8639 (mpp)
REVERT: D  152 LEU cc_start: 0.9534 (tp) cc_final: 0.9213 (tp)
REVERT: D  156 ASN cc_start: 0.9070 (m110) cc_final: 0.8858 (m110)
REVERT: D  212 MET cc_start: 0.4427 (ttt) cc_final: 0.3956 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 350
  average time/residue: 0.0952
  time to fit residues: 46.0703
Evaluate side-chains
  287 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 104 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 102 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 109 optimal weight:    7.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.120281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.096293 restraints weight = 32813.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.099354 restraints weight = 22116.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.101660 restraints weight = 16256.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.103287 restraints weight = 12666.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.104632 restraints weight = 10379.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.6290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   9970  Z= 0.217
  Angle     :  0.855  10.554  13514  Z= 0.465
  Chirality :  0.047   0.265   1563
  Planarity :  0.007   0.157   1689
  Dihedral  : 11.258 116.152   1464
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 20.65
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.28 %
    Favored  : 89.39 %
  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 : 3.03 %
    Twisted General : 0.60 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.24), residues: 1197
  helix: -0.18 (0.19), residues: 694
  sheet:  0.93 (0.47), residues: 110
  loop : -2.64 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  95 
 TYR   0.030   0.002   TYR B  98 
 PHE   0.038   0.003   PHE B  66 
 TRP   0.034   0.003   TRP D  92 
 HIS   0.009   0.002   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 9970)
  covalent geometry    : angle       0.85522 (13514)
  hydrogen bonds       : bond        0.06019 (  595)
  hydrogen bonds       : angle       6.49648 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 332
  time to evaluate  : 0.426 
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   19 MET cc_start: 0.8722 (pmm) cc_final: 0.8512 (pmm)
REVERT: A   44 TYR cc_start: 0.5896 (m-80) cc_final: 0.5598 (m-80)
REVERT: A   76 MET cc_start: 0.8633 (tmm) cc_final: 0.7869 (tmm)
REVERT: A   77 LEU cc_start: 0.9088 (mt) cc_final: 0.8569 (mt)
REVERT: A   98 TYR cc_start: 0.7879 (t80) cc_final: 0.7653 (t80)
REVERT: A  109 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8504 (ttpp)
REVERT: A  116 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.7755 (mmp80)
REVERT: A  118 GLU cc_start: 0.8923 (pt0) cc_final: 0.8628 (pt0)
REVERT: A  132 ARG cc_start: 0.8778 (mtm110) cc_final: 0.8488 (mtm180)
REVERT: A  153 PHE cc_start: 0.9203 (t80) cc_final: 0.8928 (t80)
REVERT: A  179 HIS cc_start: 0.8294 (m-70) cc_final: 0.7973 (m-70)
REVERT: A  204 MET cc_start: 0.8420 (tpp) cc_final: 0.7750 (tpp)
REVERT: A  211 LYS cc_start: 0.9138 (mttt) cc_final: 0.8649 (mttt)
REVERT: A  213 LEU cc_start: 0.8907 (tt) cc_final: 0.8697 (tt)
REVERT: A  246 ILE cc_start: 0.9742 (mm) cc_final: 0.9461 (tp)
REVERT: A  327 HIS cc_start: 0.7623 (m170) cc_final: 0.6623 (m-70)
REVERT: A  372 GLU cc_start: 0.9214 (mp0) cc_final: 0.8887 (mp0)
REVERT: B   19 MET cc_start: 0.8175 (pmm) cc_final: 0.7489 (pmm)
REVERT: B   55 LEU cc_start: 0.9168 (mt) cc_final: 0.8806 (mt)
REVERT: B   57 ILE cc_start: 0.9008 (tt) cc_final: 0.8769 (tt)
REVERT: B   74 LEU cc_start: 0.9343 (mt) cc_final: 0.9130 (mt)
REVERT: B   78 CYS cc_start: 0.8754 (p) cc_final: 0.8478 (p)
REVERT: B   88 LYS cc_start: 0.9478 (tttt) cc_final: 0.9120 (tptp)
REVERT: B  100 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8734 (tp30)
REVERT: B  198 MET cc_start: 0.8252 (mmt) cc_final: 0.8011 (mmt)
REVERT: B  201 PHE cc_start: 0.8369 (m-10) cc_final: 0.7709 (m-80)
REVERT: B  252 ASP cc_start: 0.9274 (t0) cc_final: 0.8967 (t70)
REVERT: B  327 HIS cc_start: 0.8482 (m170) cc_final: 0.8203 (m170)
REVERT: B  340 TYR cc_start: 0.8967 (m-80) cc_final: 0.8680 (m-80)
REVERT: B  363 LEU cc_start: 0.9369 (mt) cc_final: 0.9006 (mt)
REVERT: B  376 LEU cc_start: 0.9686 (mt) cc_final: 0.9127 (mt)
REVERT: C   52 LYS cc_start: 0.6630 (mttm) cc_final: 0.6211 (mmmt)
REVERT: C  159 LYS cc_start: 0.8031 (mttt) cc_final: 0.7765 (tptp)
REVERT: C  163 LYS cc_start: 0.7480 (tttt) cc_final: 0.6726 (pttt)
REVERT: C  191 THR cc_start: 0.8988 (m) cc_final: 0.8599 (p)
REVERT: C  198 LEU cc_start: 0.9249 (tp) cc_final: 0.8900 (tp)
REVERT: C  200 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7965 (mt-10)
REVERT: C  213 LYS cc_start: 0.9011 (tttt) cc_final: 0.8670 (tmtt)
REVERT: C  222 LEU cc_start: 0.9307 (pp) cc_final: 0.8996 (tt)
REVERT: D   35 ILE cc_start: 0.8500 (mp) cc_final: 0.7928 (mp)
REVERT: D   46 GLU cc_start: 0.8364 (tt0) cc_final: 0.7766 (pm20)
REVERT: D  109 GLN cc_start: 0.8871 (mp10) cc_final: 0.8644 (mp10)
REVERT: D  124 ASP cc_start: 0.9664 (m-30) cc_final: 0.9277 (m-30)
REVERT: D  147 LEU cc_start: 0.8578 (mt) cc_final: 0.8224 (mt)
REVERT: D  149 MET cc_start: 0.9167 (mpp) cc_final: 0.8460 (mpp)
REVERT: D  187 THR cc_start: 0.8636 (m) cc_final: 0.7975 (m)
REVERT: D  212 MET cc_start: 0.4299 (ttt) cc_final: 0.3736 (ptt)
  outliers start: 2
  outliers final: 0
  residues processed: 332
  average time/residue: 0.0948
  time to fit residues: 43.9108
Evaluate side-chains
  279 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 101 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 HIS
B 220 HIS
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** 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 = 0.3912 r_free = 0.3912 target = 0.122315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.098336 restraints weight = 32112.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.101592 restraints weight = 21263.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.104020 restraints weight = 15406.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.105746 restraints weight = 11860.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.106973 restraints weight = 9633.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.6683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   9970  Z= 0.183
  Angle     :  0.829  10.277  13514  Z= 0.446
  Chirality :  0.046   0.274   1563
  Planarity :  0.007   0.154   1689
  Dihedral  : 11.105 109.914   1464
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 19.07
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.19 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.33 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.24), residues: 1197
  helix: -0.21 (0.19), residues: 696
  sheet:  0.92 (0.48), residues: 110
  loop : -2.55 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 398 
 TYR   0.028   0.002   TYR B  98 
 PHE   0.029   0.002   PHE A 201 
 TRP   0.029   0.003   TRP C 125 
 HIS   0.014   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 9970)
  covalent geometry    : angle       0.82933 (13514)
  hydrogen bonds       : bond        0.05683 (  595)
  hydrogen bonds       : angle       6.47720 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 345
  time to evaluate  : 0.390 
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: A   19 MET cc_start: 0.8728 (pmm) cc_final: 0.8489 (pmm)
REVERT: A   44 TYR cc_start: 0.5908 (m-80) cc_final: 0.5666 (m-80)
REVERT: A   76 MET cc_start: 0.8616 (tmm) cc_final: 0.7792 (tmm)
REVERT: A   77 LEU cc_start: 0.9124 (mt) cc_final: 0.8600 (mt)
REVERT: A  109 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8448 (ttpp)
REVERT: A  116 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.7968 (mmt-90)
REVERT: A  132 ARG cc_start: 0.8828 (mtm110) cc_final: 0.8545 (mtm180)
REVERT: A  153 PHE cc_start: 0.9146 (t80) cc_final: 0.8734 (t80)
REVERT: A  179 HIS cc_start: 0.8382 (m-70) cc_final: 0.8106 (m-70)
REVERT: A  204 MET cc_start: 0.8320 (tpp) cc_final: 0.7539 (tpp)
REVERT: A  211 LYS cc_start: 0.9087 (mttt) cc_final: 0.8614 (mttt)
REVERT: A  372 GLU cc_start: 0.9050 (mp0) cc_final: 0.8748 (mp0)
REVERT: A  376 LEU cc_start: 0.9661 (mm) cc_final: 0.9393 (mm)
REVERT: A  380 HIS cc_start: 0.9276 (m-70) cc_final: 0.8713 (m-70)
REVERT: B   19 MET cc_start: 0.8266 (pmm) cc_final: 0.7589 (pmm)
REVERT: B   55 LEU cc_start: 0.9197 (mt) cc_final: 0.8903 (mt)
REVERT: B   57 ILE cc_start: 0.8942 (tt) cc_final: 0.8714 (tt)
REVERT: B   74 LEU cc_start: 0.9362 (mt) cc_final: 0.9137 (mt)
REVERT: B   78 CYS cc_start: 0.8698 (p) cc_final: 0.8450 (p)
REVERT: B   88 LYS cc_start: 0.9449 (tttt) cc_final: 0.9089 (tptp)
REVERT: B  100 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8730 (tp30)
REVERT: B  179 HIS cc_start: 0.8598 (m-70) cc_final: 0.8358 (m-70)
REVERT: B  198 MET cc_start: 0.8186 (mmt) cc_final: 0.7875 (mmt)
REVERT: B  307 ASN cc_start: 0.8207 (m110) cc_final: 0.7612 (t0)
REVERT: B  363 LEU cc_start: 0.9323 (mt) cc_final: 0.8954 (mt)
REVERT: B  376 LEU cc_start: 0.9642 (mt) cc_final: 0.9264 (mt)
REVERT: B  380 HIS cc_start: 0.8989 (m90) cc_final: 0.8457 (m90)
REVERT: C   42 TRP cc_start: 0.8721 (t60) cc_final: 0.8164 (t60)
REVERT: C   52 LYS cc_start: 0.6622 (mttm) cc_final: 0.6213 (mmmt)
REVERT: C   58 HIS cc_start: 0.9105 (m170) cc_final: 0.8881 (m170)
REVERT: C  159 LYS cc_start: 0.7961 (mttt) cc_final: 0.7678 (tptp)
REVERT: C  160 PHE cc_start: 0.8702 (t80) cc_final: 0.8050 (t80)
REVERT: C  163 LYS cc_start: 0.7618 (tttt) cc_final: 0.6850 (pttt)
REVERT: C  213 LYS cc_start: 0.8944 (tttt) cc_final: 0.8594 (tmtt)
REVERT: C  222 LEU cc_start: 0.9309 (pp) cc_final: 0.9069 (tt)
REVERT: D  124 ASP cc_start: 0.9625 (m-30) cc_final: 0.9325 (m-30)
REVERT: D  133 HIS cc_start: 0.8870 (p90) cc_final: 0.8669 (p90)
REVERT: D  147 LEU cc_start: 0.8627 (mt) cc_final: 0.8238 (mt)
REVERT: D  149 MET cc_start: 0.8980 (mpp) cc_final: 0.8302 (mpp)
REVERT: D  187 THR cc_start: 0.8787 (m) cc_final: 0.7930 (m)
REVERT: D  212 MET cc_start: 0.4222 (ttt) cc_final: 0.3595 (ptt)
  outliers start: 3
  outliers final: 0
  residues processed: 348
  average time/residue: 0.0935
  time to fit residues: 45.7842
Evaluate side-chains
  290 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   chunk 98 optimal weight:    7.9990
   chunk 71 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 40 optimal weight:    0.3980
   chunk 86 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   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  45 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 HIS
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 335 ASN
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.125327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.100730 restraints weight = 31618.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.103964 restraints weight = 21155.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.106355 restraints weight = 15452.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.108106 restraints weight = 11993.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.109374 restraints weight = 9782.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.7105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   9970  Z= 0.170
  Angle     :  0.815  13.070  13514  Z= 0.439
  Chirality :  0.046   0.279   1563
  Planarity :  0.006   0.151   1689
  Dihedral  : 10.836 102.042   1464
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 18.26
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.77 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.13 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.51 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.24), residues: 1197
  helix: -0.23 (0.19), residues: 700
  sheet:  0.82 (0.48), residues: 110
  loop : -2.65 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  95 
 TYR   0.025   0.002   TYR B  98 
 PHE   0.042   0.002   PHE B  66 
 TRP   0.022   0.002   TRP D  92 
 HIS   0.007   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9970)
  covalent geometry    : angle       0.81546 (13514)
  hydrogen bonds       : bond        0.05549 (  595)
  hydrogen bonds       : angle       6.26670 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 338
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 GLN cc_start: 0.9462 (mt0) cc_final: 0.9122 (mm-40)
REVERT: A  109 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8521 (ttpp)
REVERT: A  132 ARG cc_start: 0.8820 (mtm110) cc_final: 0.8588 (mtm180)
REVERT: A  153 PHE cc_start: 0.9143 (t80) cc_final: 0.8758 (t80)
REVERT: A  174 ARG cc_start: 0.9216 (mtp180) cc_final: 0.8923 (mtp180)
REVERT: A  179 HIS cc_start: 0.8190 (m-70) cc_final: 0.7938 (m-70)
REVERT: A  200 ILE cc_start: 0.9454 (tp) cc_final: 0.9210 (tt)
REVERT: A  204 MET cc_start: 0.8399 (tpp) cc_final: 0.7361 (tpp)
REVERT: A  211 LYS cc_start: 0.9083 (mttt) cc_final: 0.8480 (mttm)
REVERT: A  244 LEU cc_start: 0.5146 (mt) cc_final: 0.4800 (mm)
REVERT: A  248 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8532 (mttp)
REVERT: A  372 GLU cc_start: 0.8974 (mp0) cc_final: 0.8655 (mp0)
REVERT: B   19 MET cc_start: 0.8179 (pmm) cc_final: 0.7040 (pmm)
REVERT: B   55 LEU cc_start: 0.9118 (mt) cc_final: 0.8858 (mt)
REVERT: B   57 ILE cc_start: 0.8900 (tt) cc_final: 0.8652 (tt)
REVERT: B   78 CYS cc_start: 0.8731 (p) cc_final: 0.8481 (p)
REVERT: B   88 LYS cc_start: 0.9446 (tttt) cc_final: 0.9072 (tptp)
REVERT: B  100 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8678 (tp30)
REVERT: B  110 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8988 (tppt)
REVERT: B  151 LEU cc_start: 0.9516 (mt) cc_final: 0.9222 (pp)
REVERT: B  179 HIS cc_start: 0.8605 (m-70) cc_final: 0.8172 (m-70)
REVERT: B  187 TYR cc_start: 0.7491 (t80) cc_final: 0.7172 (t80)
REVERT: B  197 MET cc_start: 0.7302 (ptp) cc_final: 0.5861 (ptp)
REVERT: B  198 MET cc_start: 0.8209 (mmt) cc_final: 0.7786 (mmt)
REVERT: B  307 ASN cc_start: 0.8175 (m110) cc_final: 0.7685 (t0)
REVERT: B  363 LEU cc_start: 0.9337 (mt) cc_final: 0.8936 (mt)
REVERT: B  370 ASP cc_start: 0.8777 (t0) cc_final: 0.8368 (p0)
REVERT: B  376 LEU cc_start: 0.9682 (mt) cc_final: 0.9289 (mt)
REVERT: B  380 HIS cc_start: 0.9053 (m90) cc_final: 0.8493 (m-70)
REVERT: B  400 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9099 (mm-30)
REVERT: C   42 TRP cc_start: 0.8548 (t60) cc_final: 0.8263 (t-100)
REVERT: C   52 LYS cc_start: 0.6636 (mttm) cc_final: 0.6294 (mmmt)
REVERT: C   70 SER cc_start: 0.9378 (t) cc_final: 0.9137 (p)
REVERT: C  159 LYS cc_start: 0.7908 (mttt) cc_final: 0.7642 (tptp)
REVERT: C  160 PHE cc_start: 0.8736 (t80) cc_final: 0.8131 (t80)
REVERT: C  163 LYS cc_start: 0.7492 (tttt) cc_final: 0.6775 (pttt)
REVERT: C  213 LYS cc_start: 0.8851 (tttt) cc_final: 0.8502 (tmtt)
REVERT: C  222 LEU cc_start: 0.9310 (pp) cc_final: 0.9043 (tt)
REVERT: D   95 ARG cc_start: 0.7706 (ptt180) cc_final: 0.7468 (ptt180)
REVERT: D  109 GLN cc_start: 0.9211 (mp10) cc_final: 0.8833 (mp10)
REVERT: D  124 ASP cc_start: 0.9640 (m-30) cc_final: 0.9280 (m-30)
REVERT: D  140 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7680 (ptp90)
REVERT: D  147 LEU cc_start: 0.8642 (mt) cc_final: 0.8276 (mt)
REVERT: D  149 MET cc_start: 0.8875 (mpp) cc_final: 0.8142 (mpp)
REVERT: D  212 MET cc_start: 0.3221 (ttt) cc_final: 0.2902 (ptt)
  outliers start: 1
  outliers final: 1
  residues processed: 339
  average time/residue: 0.0961
  time to fit residues: 45.1037
Evaluate side-chains
  292 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 291
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.0370
   chunk 68 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 89 optimal weight:    0.0070
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.0082

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 HIS
** B 196 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**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS
** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.126209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.101573 restraints weight = 31890.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.104824 restraints weight = 21388.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.107190 restraints weight = 15606.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.108861 restraints weight = 12140.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.110212 restraints weight = 9968.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.7396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.094   9970  Z= 0.167
  Angle     :  0.809  13.799  13514  Z= 0.434
  Chirality :  0.046   0.277   1563
  Planarity :  0.006   0.152   1689
  Dihedral  : 10.655  87.833   1464
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 17.70
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.44 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.24), residues: 1197
  helix: -0.26 (0.19), residues: 699
  sheet:  0.66 (0.54), residues: 97
  loop : -2.41 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  95 
 TYR   0.025   0.002   TYR B  98 
 PHE   0.033   0.002   PHE A 201 
 TRP   0.020   0.002   TRP B 191 
 HIS   0.012   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9970)
  covalent geometry    : angle       0.80943 (13514)
  hydrogen bonds       : bond        0.05381 (  595)
  hydrogen bonds       : angle       6.27262 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 346
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8358 (ttpp)
REVERT: A  116 ARG cc_start: 0.8340 (mpt180) cc_final: 0.8114 (mmt-90)
REVERT: A  132 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8520 (mtm180)
REVERT: A  153 PHE cc_start: 0.9031 (t80) cc_final: 0.8641 (t80)
REVERT: A  174 ARG cc_start: 0.9223 (mtp180) cc_final: 0.8593 (mtp180)
REVERT: A  200 ILE cc_start: 0.9435 (tp) cc_final: 0.9177 (tt)
REVERT: A  204 MET cc_start: 0.8406 (tpp) cc_final: 0.7332 (tpp)
REVERT: A  209 LEU cc_start: 0.9475 (pt) cc_final: 0.9255 (pp)
REVERT: A  211 LYS cc_start: 0.9114 (mttt) cc_final: 0.8515 (mttm)
REVERT: A  213 LEU cc_start: 0.8966 (tt) cc_final: 0.8686 (tt)
REVERT: A  217 GLN cc_start: 0.9419 (mp10) cc_final: 0.9151 (mp10)
REVERT: A  244 LEU cc_start: 0.5058 (mt) cc_final: 0.4725 (mm)
REVERT: A  248 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8410 (mttp)
REVERT: A  361 ARG cc_start: 0.9171 (mtm180) cc_final: 0.8675 (mtt180)
REVERT: A  372 GLU cc_start: 0.8929 (mp0) cc_final: 0.8539 (mp0)
REVERT: B   19 MET cc_start: 0.8185 (pmm) cc_final: 0.7127 (pmm)
REVERT: B   20 ASP cc_start: 0.7625 (m-30) cc_final: 0.6571 (m-30)
REVERT: B   55 LEU cc_start: 0.9116 (mt) cc_final: 0.8879 (mt)
REVERT: B   57 ILE cc_start: 0.8913 (tt) cc_final: 0.8683 (tt)
REVERT: B   74 LEU cc_start: 0.9411 (mt) cc_final: 0.9148 (mt)
REVERT: B   78 CYS cc_start: 0.8793 (p) cc_final: 0.8583 (p)
REVERT: B   88 LYS cc_start: 0.9438 (tttt) cc_final: 0.9086 (tptp)
REVERT: B  100 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8451 (mm-30)
REVERT: B  187 TYR cc_start: 0.7395 (t80) cc_final: 0.7135 (t80)
REVERT: B  198 MET cc_start: 0.8255 (mmt) cc_final: 0.7949 (mmt)
REVERT: B  307 ASN cc_start: 0.7876 (m110) cc_final: 0.7553 (t0)
REVERT: B  363 LEU cc_start: 0.9321 (mt) cc_final: 0.8889 (mt)
REVERT: B  370 ASP cc_start: 0.8907 (t0) cc_final: 0.8516 (p0)
REVERT: B  376 LEU cc_start: 0.9666 (mt) cc_final: 0.9221 (mt)
REVERT: B  377 MET cc_start: 0.9493 (ttm) cc_final: 0.8923 (tmm)
REVERT: B  380 HIS cc_start: 0.9103 (m90) cc_final: 0.8523 (m-70)
REVERT: B  400 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9132 (mm-30)
REVERT: C   42 TRP cc_start: 0.8631 (t60) cc_final: 0.8336 (t-100)
REVERT: C   70 SER cc_start: 0.9428 (t) cc_final: 0.9182 (p)
REVERT: C  159 LYS cc_start: 0.7873 (mttt) cc_final: 0.7637 (tptp)
REVERT: C  160 PHE cc_start: 0.8724 (t80) cc_final: 0.8155 (t80)
REVERT: C  163 LYS cc_start: 0.7564 (tttt) cc_final: 0.6882 (pttt)
REVERT: C  213 LYS cc_start: 0.8775 (tttt) cc_final: 0.8447 (tmtt)
REVERT: C  218 LYS cc_start: 0.7572 (mppt) cc_final: 0.6321 (mppt)
REVERT: C  222 LEU cc_start: 0.9323 (pp) cc_final: 0.9019 (tt)
REVERT: D   95 ARG cc_start: 0.7744 (ptt180) cc_final: 0.7457 (ptt180)
REVERT: D  109 GLN cc_start: 0.9366 (mp10) cc_final: 0.9049 (mp10)
REVERT: D  124 ASP cc_start: 0.9667 (m-30) cc_final: 0.9313 (m-30)
REVERT: D  133 HIS cc_start: 0.8703 (p90) cc_final: 0.8492 (p90)
REVERT: D  140 ARG cc_start: 0.8127 (ptm160) cc_final: 0.7791 (ptp90)
REVERT: D  147 LEU cc_start: 0.8696 (mt) cc_final: 0.8298 (mt)
REVERT: D  149 MET cc_start: 0.8845 (mpp) cc_final: 0.8104 (mpp)
REVERT: D  157 ILE cc_start: 0.9528 (mt) cc_final: 0.8906 (mt)
REVERT: D  187 THR cc_start: 0.8460 (m) cc_final: 0.8021 (m)
REVERT: D  212 MET cc_start: 0.3678 (ttt) cc_final: 0.3237 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 346
  average time/residue: 0.0968
  time to fit residues: 46.3354
Evaluate side-chains
  298 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 88 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** 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 339 GLN
B  22 HIS
B 129 ASN
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
** D 223 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.124310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.099920 restraints weight = 31935.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.103073 restraints weight = 21398.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.105447 restraints weight = 15665.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.107180 restraints weight = 12177.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.108431 restraints weight = 9935.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.7647

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= 0.183
  Angle     :  0.832  14.909  13514  Z= 0.446
  Chirality :  0.046   0.282   1563
  Planarity :  0.007   0.153   1689
  Dihedral  : 10.689  72.063   1464
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 19.68
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.44 %
    Favored  : 89.22 %
  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 : 0.34 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.24), residues: 1197
  helix: -0.25 (0.19), residues: 696
  sheet:  0.82 (0.56), residues: 90
  loop : -2.42 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  59 
 TYR   0.026   0.002   TYR B  98 
 PHE   0.043   0.002   PHE B  66 
 TRP   0.021   0.002   TRP B 191 
 HIS   0.024   0.002   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9970)
  covalent geometry    : angle       0.83168 (13514)
  hydrogen bonds       : bond        0.05567 (  595)
  hydrogen bonds       : angle       6.32125 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 333
  time to evaluate  : 0.392 
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: A   76 MET cc_start: 0.8685 (tmm) cc_final: 0.8185 (tmm)
REVERT: A   77 LEU cc_start: 0.9101 (mt) cc_final: 0.8545 (mt)
REVERT: A  109 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8254 (ttpp)
REVERT: A  132 ARG cc_start: 0.8842 (mtm110) cc_final: 0.8525 (mtm180)
REVERT: A  153 PHE cc_start: 0.9086 (t80) cc_final: 0.8713 (t80)
REVERT: A  174 ARG cc_start: 0.9256 (mtp180) cc_final: 0.8656 (mtp180)
REVERT: A  179 HIS cc_start: 0.8045 (m-70) cc_final: 0.7796 (m-70)
REVERT: A  200 ILE cc_start: 0.9420 (tp) cc_final: 0.9182 (tt)
REVERT: A  204 MET cc_start: 0.8337 (tpp) cc_final: 0.8029 (tpp)
REVERT: A  213 LEU cc_start: 0.8982 (tt) cc_final: 0.8731 (tt)
REVERT: A  361 ARG cc_start: 0.9221 (mtm180) cc_final: 0.8674 (mtt180)
REVERT: A  372 GLU cc_start: 0.8954 (mp0) cc_final: 0.8581 (mp0)
REVERT: B   19 MET cc_start: 0.8046 (pmm) cc_final: 0.7149 (pmm)
REVERT: B   20 ASP cc_start: 0.7622 (m-30) cc_final: 0.6572 (m-30)
REVERT: B   55 LEU cc_start: 0.9125 (mt) cc_final: 0.8857 (mt)
REVERT: B   74 LEU cc_start: 0.9405 (mt) cc_final: 0.9142 (mt)
REVERT: B   78 CYS cc_start: 0.8792 (p) cc_final: 0.8581 (p)
REVERT: B   88 LYS cc_start: 0.9449 (tttt) cc_final: 0.9078 (tptp)
REVERT: B  100 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8482 (mm-30)
REVERT: B  110 LYS cc_start: 0.9281 (mmpt) cc_final: 0.9078 (mmmt)
REVERT: B  153 PHE cc_start: 0.8797 (t80) cc_final: 0.8590 (t80)
REVERT: B  174 ARG cc_start: 0.9220 (mtt180) cc_final: 0.8798 (ptp-170)
REVERT: B  187 TYR cc_start: 0.7574 (t80) cc_final: 0.7238 (t80)
REVERT: B  198 MET cc_start: 0.8151 (mmt) cc_final: 0.7841 (mmt)
REVERT: B  307 ASN cc_start: 0.7869 (m110) cc_final: 0.7509 (t0)
REVERT: B  341 GLN cc_start: 0.8929 (pm20) cc_final: 0.8712 (pm20)
REVERT: B  370 ASP cc_start: 0.8853 (t0) cc_final: 0.8468 (p0)
REVERT: B  400 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9120 (mm-30)
REVERT: C   42 TRP cc_start: 0.8667 (t60) cc_final: 0.7978 (t60)
REVERT: C   70 SER cc_start: 0.9455 (t) cc_final: 0.9178 (p)
REVERT: C  159 LYS cc_start: 0.8122 (mttt) cc_final: 0.7887 (tptp)
REVERT: C  160 PHE cc_start: 0.8738 (t80) cc_final: 0.8178 (t80)
REVERT: C  163 LYS cc_start: 0.7576 (tttt) cc_final: 0.6908 (pttt)
REVERT: C  213 LYS cc_start: 0.8775 (tttt) cc_final: 0.8508 (tmtt)
REVERT: C  218 LYS cc_start: 0.7651 (mppt) cc_final: 0.6344 (mppt)
REVERT: C  222 LEU cc_start: 0.9310 (pp) cc_final: 0.9056 (tt)
REVERT: D  109 GLN cc_start: 0.9375 (mp10) cc_final: 0.9150 (pm20)
REVERT: D  113 GLU cc_start: 0.8239 (tp30) cc_final: 0.7956 (tp30)
REVERT: D  115 LEU cc_start: 0.9135 (mp) cc_final: 0.8342 (tt)
REVERT: D  124 ASP cc_start: 0.9655 (m-30) cc_final: 0.9294 (m-30)
REVERT: D  140 ARG cc_start: 0.8018 (ptm160) cc_final: 0.7648 (ptp90)
REVERT: D  149 MET cc_start: 0.8714 (mpp) cc_final: 0.7912 (mpp)
REVERT: D  212 MET cc_start: 0.3117 (ttt) cc_final: 0.2716 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 333
  average time/residue: 0.0928
  time to fit residues: 43.3519
Evaluate side-chains
  286 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 286
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 93 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 HIS
B 129 ASN
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 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**
D 186 HIS
D 223 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.121341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.097076 restraints weight = 32808.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.100110 restraints weight = 22236.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.102374 restraints weight = 16408.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.104050 restraints weight = 12837.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.105294 restraints weight = 10543.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.7754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   9970  Z= 0.213
  Angle     :  0.881  18.087  13514  Z= 0.472
  Chirality :  0.048   0.279   1563
  Planarity :  0.007   0.153   1689
  Dihedral  : 10.862  70.033   1464
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 21.88
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.11 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.61 (0.23), residues: 1197
  helix: -0.41 (0.19), residues: 694
  sheet:  0.73 (0.56), residues: 90
  loop : -2.56 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 192 
 TYR   0.027   0.002   TYR B  98 
 PHE   0.031   0.003   PHE B  66 
 TRP   0.021   0.003   TRP B 191 
 HIS   0.016   0.002   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 9970)
  covalent geometry    : angle       0.88105 (13514)
  hydrogen bonds       : bond        0.05758 (  595)
  hydrogen bonds       : angle       6.52557 ( 1728)

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 330
  time to evaluate  : 0.391 
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: A   44 TYR cc_start: 0.5353 (m-80) cc_final: 0.5114 (m-80)
REVERT: A   76 MET cc_start: 0.8686 (tmm) cc_final: 0.8228 (tmm)
REVERT: A   77 LEU cc_start: 0.9137 (mt) cc_final: 0.8586 (mt)
REVERT: A  109 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8453 (ttpp)
REVERT: A  116 ARG cc_start: 0.8319 (mpt180) cc_final: 0.8100 (mmt-90)
REVERT: A  132 ARG cc_start: 0.8865 (mtm110) cc_final: 0.8517 (mtm180)
REVERT: A  153 PHE cc_start: 0.9181 (t80) cc_final: 0.8268 (t80)
REVERT: A  174 ARG cc_start: 0.9233 (mtp180) cc_final: 0.8602 (mtp180)
REVERT: A  200 ILE cc_start: 0.9470 (tp) cc_final: 0.9160 (tt)
REVERT: A  204 MET cc_start: 0.8629 (tpp) cc_final: 0.8362 (tpp)
REVERT: A  214 LEU cc_start: 0.9239 (mt) cc_final: 0.9023 (mt)
REVERT: A  217 GLN cc_start: 0.9507 (mp10) cc_final: 0.9029 (mp10)
REVERT: A  361 ARG cc_start: 0.9256 (mtm180) cc_final: 0.8683 (mtt180)
REVERT: A  372 GLU cc_start: 0.8985 (mp0) cc_final: 0.8669 (mp0)
REVERT: B   19 MET cc_start: 0.7760 (pmm) cc_final: 0.6897 (pmm)
REVERT: B   20 ASP cc_start: 0.7502 (m-30) cc_final: 0.6519 (m-30)
REVERT: B   55 LEU cc_start: 0.9129 (mt) cc_final: 0.8898 (mt)
REVERT: B   74 LEU cc_start: 0.9411 (mt) cc_final: 0.9112 (mt)
REVERT: B   78 CYS cc_start: 0.8782 (p) cc_final: 0.8546 (p)
REVERT: B   88 LYS cc_start: 0.9452 (tttt) cc_final: 0.9084 (tptp)
REVERT: B  100 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8638 (tp30)
REVERT: B  174 ARG cc_start: 0.9100 (mtt180) cc_final: 0.8741 (ptp-170)
REVERT: B  187 TYR cc_start: 0.7783 (t80) cc_final: 0.7407 (t80)
REVERT: B  198 MET cc_start: 0.8275 (mmt) cc_final: 0.7954 (mmt)
REVERT: B  208 PHE cc_start: 0.8936 (p90) cc_final: 0.8497 (p90)
REVERT: B  252 ASP cc_start: 0.9188 (t0) cc_final: 0.8976 (t0)
REVERT: B  307 ASN cc_start: 0.7945 (m110) cc_final: 0.7358 (t0)
REVERT: B  359 GLU cc_start: 0.8813 (tt0) cc_final: 0.8568 (tt0)
REVERT: B  370 ASP cc_start: 0.8933 (t0) cc_final: 0.8543 (p0)
REVERT: B  380 HIS cc_start: 0.8868 (m90) cc_final: 0.8401 (m90)
REVERT: B  400 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9129 (mm-30)
REVERT: C   58 HIS cc_start: 0.9068 (m170) cc_final: 0.8819 (m-70)
REVERT: C   79 LEU cc_start: 0.9552 (tp) cc_final: 0.9244 (tp)
REVERT: C  159 LYS cc_start: 0.8157 (mttt) cc_final: 0.7916 (tptp)
REVERT: C  160 PHE cc_start: 0.8707 (t80) cc_final: 0.8173 (t80)
REVERT: C  163 LYS cc_start: 0.7499 (tttt) cc_final: 0.6846 (pttt)
REVERT: C  197 PHE cc_start: 0.8929 (m-80) cc_final: 0.8655 (m-80)
REVERT: C  213 LYS cc_start: 0.8846 (tttt) cc_final: 0.8586 (tmtt)
REVERT: C  222 LEU cc_start: 0.9316 (pp) cc_final: 0.8949 (tt)
REVERT: D  109 GLN cc_start: 0.9348 (mp10) cc_final: 0.9053 (mp10)
REVERT: D  113 GLU cc_start: 0.8291 (tp30) cc_final: 0.8071 (tp30)
REVERT: D  115 LEU cc_start: 0.9203 (mp) cc_final: 0.8461 (tt)
REVERT: D  124 ASP cc_start: 0.9655 (m-30) cc_final: 0.9285 (m-30)
REVERT: D  133 HIS cc_start: 0.8662 (p90) cc_final: 0.8424 (p90)
REVERT: D  140 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7645 (ptp90)
REVERT: D  147 LEU cc_start: 0.8570 (mt) cc_final: 0.8311 (mt)
REVERT: D  149 MET cc_start: 0.8897 (mpp) cc_final: 0.8138 (mpp)
REVERT: D  212 MET cc_start: 0.3076 (ttt) cc_final: 0.2551 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 330
  average time/residue: 0.0930
  time to fit residues: 43.3984
Evaluate side-chains
  283 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** 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 353 GLN
** B  22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 129 ASN
** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 103 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.119594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.095973 restraints weight = 33240.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.098992 restraints weight = 22360.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.101216 restraints weight = 16416.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.102784 restraints weight = 12830.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.104068 restraints weight = 10559.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.7851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   9970  Z= 0.227
  Angle     :  0.904  19.491  13514  Z= 0.488
  Chirality :  0.049   0.280   1563
  Planarity :  0.007   0.153   1689
  Dihedral  : 10.945  74.539   1464
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 22.74
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.78 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.34 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.23), residues: 1197
  helix: -0.58 (0.19), residues: 692
  sheet:  0.78 (0.49), residues: 110
  loop : -2.86 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 192 
 TYR   0.029   0.003   TYR B  98 
 PHE   0.032   0.003   PHE B  66 
 TRP   0.020   0.003   TRP D  69 
 HIS   0.014   0.002   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9970)
  covalent geometry    : angle       0.90418 (13514)
  hydrogen bonds       : bond        0.05919 (  595)
  hydrogen bonds       : angle       6.69559 ( 1728)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1771.15 seconds
wall clock time: 31 minutes 31.58 seconds (1891.58 seconds total)