Starting phenix.real_space_refine
on Fri Feb 14 05:51:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9j_39081/02_2025/8y9j_39081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9j_39081/02_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_39081/02_2025/8y9j_39081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9j_39081/02_2025/8y9j_39081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9j_39081/02_2025/8y9j_39081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9j_39081/02_2025/8y9j_39081.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9770
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3071
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 8, 'TRANS': 381}
    Chain: "B"
      Number of atoms: 3066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3066
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 8, 'TRANS': 380}
    Chain: "C"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1764
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 9, 'TRANS': 212}
    Chain: "D"
      Number of atoms: 1629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1629
          Classifications: {'peptide': 204}
          Link IDs: {'PTRANS': 8, 'TRANS': 195}
    Chain: "K"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 240
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
  Time building chain proxies: 6.01, per 1000 atoms: 0.62
  Number of scatterers: 9770
  At special positions: 0
  Unit cell: (116.325, 120.037, 106.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P      12     15.00
     O    1823      8.00
     N    1704      7.00
     C    6190      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.55
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      69.2% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 29
    Processing helix  chain 'A' and resid 48 through 64
      removed outlier: 3.952A  pdb=" N   ILE A  52 " --> pdb=" O   ASN A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 84
      removed outlier: 3.808A  pdb=" N   GLN A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 91
      removed outlier: 4.239A  pdb=" N   LEU A  89 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 124 through 137
      removed outlier: 4.138A  pdb=" N   ASN A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ILE A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 157
      removed outlier: 3.852A  pdb=" N   PHE A 157 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 183
      removed outlier: 4.021A  pdb=" N   LEU A 169 " --> pdb=" O   GLU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 221
      removed outlier: 4.249A  pdb=" N   GLN A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   HIS A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   MET A 198 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG A 202 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG A 205 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   THR A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   LEU A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ILE A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
      removed outlier: 3.821A  pdb=" N   ALA A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 290
      removed outlier: 3.714A  pdb=" N   GLU A 276 " --> pdb=" O   LYS A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.648A  pdb=" N   ARG A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU A 299 " --> pdb=" O   PRO A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 308
      removed outlier: 3.665A  pdb=" N   ASN A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 329
    Processing helix  chain 'A' and resid 330 through 335
      removed outlier: 3.594A  pdb=" N   GLY A 333 " --> pdb=" O   THR A 330 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ASN A 335 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 366
      removed outlier: 3.523A  pdb=" N   LEU A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASP A 364 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 408
    Processing helix  chain 'B' and resid 21 through 28
      removed outlier: 4.120A  pdb=" N   LEU B  25 " --> pdb=" O   TYR B  21 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY B  28 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 64
      removed outlier: 3.827A  pdb=" N   VAL B  64 " --> pdb=" O   PHE B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 83
    Processing helix  chain 'B' and resid 85 through 93
      removed outlier: 4.215A  pdb=" N   LEU B  89 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 115 through 121
    Processing helix  chain 'B' and resid 124 through 137
      removed outlier: 3.790A  pdb=" N   ASN B 129 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG B 132 " --> pdb=" O   LYS B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 157
      removed outlier: 4.017A  pdb=" N   PHE B 157 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 183
      removed outlier: 5.012A  pdb=" N   LYS B 166 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B 169 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 221
      removed outlier: 3.610A  pdb=" N   ARG B 202 " --> pdb=" O   MET B 198 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG B 205 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE B 208 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   LEU B 209 " --> pdb=" O   ARG B 205 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 240
    Processing helix  chain 'B' and resid 244 through 253
    Processing helix  chain 'B' and resid 270 through 291
      removed outlier: 3.875A  pdb=" N   LYS B 289 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   HIS B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
      Proline residue:  B 295  - end of helix
      No H-bonds generated for 'chain 'B' and resid 292 through 297'
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.933A  pdb=" N   ASN B 307 " --> pdb=" O   GLY B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 329
      removed outlier: 3.624A  pdb=" N   HIS B 327 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 335
      removed outlier: 3.587A  pdb=" N   ASN B 335 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 367
      removed outlier: 4.720A  pdb=" N   LEU B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLY B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 407
      removed outlier: 3.756A  pdb=" N   GLU B 372 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 27
      removed outlier: 3.545A  pdb=" N   GLY C  20 " --> pdb=" O   ASP C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 62
      removed outlier: 3.873A  pdb=" N   ALA C  55 " --> pdb=" O   HIS C  51 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU C  56 " --> pdb=" O   LYS C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 76
      removed outlier: 3.693A  pdb=" N   THR C  72 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 81
    Processing helix  chain 'C' and resid 88 through 105
    Processing helix  chain 'C' and resid 115 through 130
      removed outlier: 4.454A  pdb=" N   LEU C 119 " --> pdb=" O   LEU C 115 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR C 128 " --> pdb=" O   ASP C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 144
      removed outlier: 3.900A  pdb=" N   GLN C 144 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 166
      removed outlier: 3.567A  pdb=" N   SER C 151 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 210
      removed outlier: 3.832A  pdb=" N   SER C 207 " --> pdb=" O   PRO C 204 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA C 208 " --> pdb=" O   ASP C 205 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASN C 210 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 230
      removed outlier: 3.758A  pdb=" N   LYS C 228 " --> pdb=" O   GLU C 224 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   PHE C 230 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 61
      removed outlier: 3.763A  pdb=" N   LYS D  61 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 82
      removed outlier: 3.798A  pdb=" N   ASN D  74 " --> pdb=" O   SER D  70 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU D  75 " --> pdb=" O   MET D  71 " (cutoff:3.500A)
      Proline residue:  D  77  - end of helix
    Processing helix  chain 'D' and resid 90 through 106
    Processing helix  chain 'D' and resid 114 through 128
      removed outlier: 3.852A  pdb=" N   ALA D 118 " --> pdb=" O   PRO D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 144
    Processing helix  chain 'D' and resid 145 through 166
      removed outlier: 4.085A  pdb=" N   MET D 149 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA D 166 " --> pdb=" O   ASN D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 211
    Processing helix  chain 'D' and resid 223 through 230
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44
      removed outlier: 5.937A  pdb=" N   ARG A  39 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   GLU A 107 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE A  41 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   LYS A 109 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL A  43 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257
    Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 45
      removed outlier: 6.435A  pdb=" N   ARG B  39 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   GLU B 107 " --> pdb=" O   ARG B  39 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ILE B  41 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   LYS B 109 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   VAL B  43 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 258
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 34
    Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 87
      removed outlier: 6.882A  pdb=" N   THR C  86 " --> pdb=" O   PHE C 219 " (cutoff:3.500A)
      removed outlier: 8.794A  pdb=" N   LEU C 221 " --> pdb=" O   THR C  86 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE C 179 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 33
    Processing sheet with id=AA8, first strand: chain 'D' and resid 178 through 182

    595 hydrogen bonds defined for protein.
    1728 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 2.95 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:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.300
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.390
-------------------------------------------------------------------------------
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= 0.803
  Angle     :  2.024  12.832  13514  Z= 1.393
  Chirality :  0.122   0.778   1563
  Planarity :  0.021   0.391   1689
  Dihedral  : 16.841 164.392   3789
  Min Nonbonded Distance : 2.376

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.20), residues: 1197
  helix: -1.13 (0.16), residues: 663
  sheet:  0.89 (0.50), residues: 88
  loop : -2.94 (0.26), residues: 446

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

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 443
  time to evaluate  : 1.203 
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: 0.2547
  time to fit residues: 157.0992
Evaluate side-chains
  338 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 326
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 94 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  32 GLN
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN
B 149 GLN
B 175 GLN
B 220 HIS
B 228 ASN
B 306 ASN
** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 392 ASN
C 162 ASN
** C 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS
D 202 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.127459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.101866 restraints weight = 31580.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.105221 restraints weight = 21542.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.107732 restraints weight = 15917.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   9970  Z= 0.261
  Angle     :  0.913  13.989  13514  Z= 0.493
  Chirality :  0.049   0.251   1563
  Planarity :  0.007   0.170   1689
  Dihedral  : 12.517 137.584   1464
  Min Nonbonded Distance : 2.279

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

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

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

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

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 398
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LEU cc_start: 0.9015 (mm) cc_final: 0.8797 (mm)
REVERT: A  110 LYS cc_start: 0.9261 (tptm) cc_final: 0.8928 (tppp)
REVERT: A  116 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7753 (mmp80)
REVERT: A  153 PHE cc_start: 0.9083 (t80) cc_final: 0.8428 (t80)
REVERT: A  179 HIS cc_start: 0.8535 (m-70) cc_final: 0.8182 (m-70)
REVERT: A  213 LEU cc_start: 0.9421 (tt) cc_final: 0.9179 (tt)
REVERT: A  308 LEU cc_start: 0.8687 (mm) cc_final: 0.8454 (mm)
REVERT: A  356 GLN cc_start: 0.9358 (mt0) cc_final: 0.9105 (mm110)
REVERT: A  359 GLU cc_start: 0.9250 (tt0) cc_final: 0.8995 (mt-10)
REVERT: A  362 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9282 (pp20)
REVERT: A  372 GLU cc_start: 0.9450 (mp0) cc_final: 0.9158 (mp0)
REVERT: A  376 LEU cc_start: 0.9739 (mm) cc_final: 0.9297 (mm)
REVERT: A  380 HIS cc_start: 0.9362 (m-70) cc_final: 0.8774 (m90)
REVERT: B   19 MET cc_start: 0.7590 (pmm) cc_final: 0.6885 (pmm)
REVERT: B   76 MET cc_start: 0.9279 (ptp) cc_final: 0.8985 (ptt)
REVERT: B   78 CYS cc_start: 0.8519 (p) cc_final: 0.8284 (p)
REVERT: B  221 MET cc_start: 0.7932 (ptm) cc_final: 0.7646 (ppp)
REVERT: B  363 LEU cc_start: 0.9296 (mt) cc_final: 0.9092 (mt)
REVERT: B  366 LEU cc_start: 0.7762 (tp) cc_final: 0.7513 (tt)
REVERT: B  376 LEU cc_start: 0.9694 (mt) cc_final: 0.9303 (mt)
REVERT: B  380 HIS cc_start: 0.9284 (m90) cc_final: 0.8839 (m90)
REVERT: C   42 TRP cc_start: 0.8465 (t60) cc_final: 0.7725 (t60)
REVERT: C   52 LYS cc_start: 0.6593 (mttm) cc_final: 0.6092 (mmtt)
REVERT: C  159 LYS cc_start: 0.8188 (mttt) cc_final: 0.7760 (tptp)
REVERT: C  160 PHE cc_start: 0.8752 (t80) cc_final: 0.8459 (t80)
REVERT: C  181 ILE cc_start: 0.8465 (mm) cc_final: 0.7849 (mm)
REVERT: C  191 THR cc_start: 0.9212 (m) cc_final: 0.8595 (p)
REVERT: C  198 LEU cc_start: 0.9178 (tp) cc_final: 0.8964 (tp)
REVERT: C  200 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8280 (mt-10)
REVERT: C  213 LYS cc_start: 0.8697 (tttt) cc_final: 0.8285 (pttt)
REVERT: C  222 LEU cc_start: 0.9444 (pp) cc_final: 0.9145 (tp)
REVERT: D   30 LEU cc_start: 0.8377 (mt) cc_final: 0.7654 (mp)
REVERT: D   92 TRP cc_start: 0.8656 (p-90) cc_final: 0.8260 (p-90)
REVERT: D  115 LEU cc_start: 0.9317 (mt) cc_final: 0.8678 (tt)
REVERT: D  119 LEU cc_start: 0.9660 (mt) cc_final: 0.9440 (mt)
REVERT: D  121 LEU cc_start: 0.9054 (mt) cc_final: 0.8683 (mt)
REVERT: D  124 ASP cc_start: 0.9545 (m-30) cc_final: 0.9138 (p0)
REVERT: D  149 MET cc_start: 0.9388 (mpp) cc_final: 0.9109 (mpp)
REVERT: D  152 LEU cc_start: 0.9498 (tp) cc_final: 0.9216 (tp)
REVERT: D  156 ASN cc_start: 0.9194 (m110) cc_final: 0.8918 (m110)
  outliers start: 5
  outliers final: 0
  residues processed: 398
  average time/residue: 0.2289
  time to fit residues: 124.6405
Evaluate side-chains
  307 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 306
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0770
   chunk 82 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 108 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0070
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A 192 GLN
A 196 HIS
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 353 GLN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 GLN
D 202 GLN
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.129138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.103881 restraints weight = 31143.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.107329 restraints weight = 20985.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.109888 restraints weight = 15390.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.5385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   9970  Z= 0.229
  Angle     :  0.820  12.324  13514  Z= 0.447
  Chirality :  0.046   0.241   1563
  Planarity :  0.007   0.161   1689
  Dihedral  : 11.552 134.926   1464
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.86 %
    Favored  : 90.73 %
  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 : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.24), residues: 1197
  helix:  0.16 (0.19), residues: 687
  sheet:  1.04 (0.46), residues: 112
  loop : -2.37 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  69 
 HIS   0.030   0.002   HIS B 196 
 PHE   0.045   0.003   PHE B  66 
 TYR   0.023   0.002   TYR B  98 
 ARG   0.008   0.001   ARG A 398 

*********************** 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
  370 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 367
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.8253 (pmm) cc_final: 0.8038 (pmm)
REVERT: A   51 GLU cc_start: 0.9464 (tt0) cc_final: 0.9213 (pp20)
REVERT: A   79 LEU cc_start: 0.9068 (mm) cc_final: 0.8718 (mm)
REVERT: A   96 VAL cc_start: 0.8678 (t) cc_final: 0.8137 (t)
REVERT: A   98 TYR cc_start: 0.7646 (t80) cc_final: 0.7429 (t80)
REVERT: A  109 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8149 (ttpp)
REVERT: A  116 ARG cc_start: 0.8171 (mmt-90) cc_final: 0.7658 (mmp80)
REVERT: A  179 HIS cc_start: 0.8491 (m-70) cc_final: 0.8140 (m-70)
REVERT: A  204 MET cc_start: 0.8539 (tpp) cc_final: 0.8219 (tpp)
REVERT: A  211 LYS cc_start: 0.9288 (mttt) cc_final: 0.8796 (mttt)
REVERT: A  213 LEU cc_start: 0.9394 (tt) cc_final: 0.9107 (tt)
REVERT: A  240 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7103 (mmm-85)
REVERT: A  248 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8738 (ttpt)
REVERT: A  252 ASP cc_start: 0.9305 (m-30) cc_final: 0.9058 (m-30)
REVERT: A  351 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8670 (tm-30)
REVERT: A  376 LEU cc_start: 0.9674 (mm) cc_final: 0.9309 (mm)
REVERT: A  377 MET cc_start: 0.9229 (tmm) cc_final: 0.8823 (tmm)
REVERT: A  379 PHE cc_start: 0.9415 (t80) cc_final: 0.9103 (t80)
REVERT: A  380 HIS cc_start: 0.9250 (m-70) cc_final: 0.8658 (m-70)
REVERT: B   19 MET cc_start: 0.7750 (pmm) cc_final: 0.7068 (pmm)
REVERT: B   54 GLN cc_start: 0.9467 (pp30) cc_final: 0.9167 (pp30)
REVERT: B   55 LEU cc_start: 0.9221 (mt) cc_final: 0.8793 (mt)
REVERT: B   57 ILE cc_start: 0.9024 (tt) cc_final: 0.8504 (tt)
REVERT: B   74 LEU cc_start: 0.9426 (mt) cc_final: 0.9221 (mt)
REVERT: B   78 CYS cc_start: 0.8666 (p) cc_final: 0.8440 (p)
REVERT: B  187 TYR cc_start: 0.7964 (t80) cc_final: 0.7647 (t80)
REVERT: B  196 HIS cc_start: 0.8418 (m-70) cc_final: 0.8088 (m-70)
REVERT: B  197 MET cc_start: 0.7227 (ptp) cc_final: 0.6989 (ptp)
REVERT: B  309 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8677 (mt-10)
REVERT: B  344 ARG cc_start: 0.9136 (ttt-90) cc_final: 0.8483 (mtp180)
REVERT: B  363 LEU cc_start: 0.9335 (mt) cc_final: 0.9042 (mt)
REVERT: B  366 LEU cc_start: 0.7584 (tp) cc_final: 0.6809 (tt)
REVERT: B  376 LEU cc_start: 0.9701 (mt) cc_final: 0.9229 (mt)
REVERT: C   42 TRP cc_start: 0.8435 (t60) cc_final: 0.7572 (t60)
REVERT: C   76 PHE cc_start: 0.8972 (m-80) cc_final: 0.8728 (m-80)
REVERT: C   91 LEU cc_start: 0.9278 (tp) cc_final: 0.8891 (tp)
REVERT: C  159 LYS cc_start: 0.8045 (mttt) cc_final: 0.7736 (tptp)
REVERT: C  160 PHE cc_start: 0.8849 (t80) cc_final: 0.8573 (t80)
REVERT: C  191 THR cc_start: 0.9115 (m) cc_final: 0.8554 (p)
REVERT: C  198 LEU cc_start: 0.9218 (tp) cc_final: 0.8948 (tp)
REVERT: C  200 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7978 (mt-10)
REVERT: C  222 LEU cc_start: 0.9350 (pp) cc_final: 0.9067 (tp)
REVERT: D   31 VAL cc_start: 0.8658 (p) cc_final: 0.8209 (p)
REVERT: D   46 GLU cc_start: 0.8421 (tt0) cc_final: 0.7775 (pm20)
REVERT: D  109 GLN cc_start: 0.8878 (mp10) cc_final: 0.8519 (mp10)
REVERT: D  124 ASP cc_start: 0.9626 (m-30) cc_final: 0.9313 (m-30)
REVERT: D  148 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9258 (mmmt)
REVERT: D  165 ASP cc_start: 0.9140 (m-30) cc_final: 0.8879 (m-30)
REVERT: D  201 LEU cc_start: 0.9016 (tt) cc_final: 0.8539 (mp)
REVERT: D  212 MET cc_start: 0.4894 (ttt) cc_final: 0.4566 (ptt)
  outliers start: 3
  outliers final: 1
  residues processed: 369
  average time/residue: 0.2323
  time to fit residues: 116.7051
Evaluate side-chains
  302 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 301
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 118 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 238 GLN
** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 ASN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 GLN
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  51 HIS
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
D 186 HIS
** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.121430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.097039 restraints weight = 31220.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.100269 restraints weight = 20781.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.102663 restraints weight = 15138.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.5916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   9970  Z= 0.294
  Angle     :  0.851  11.986  13514  Z= 0.460
  Chirality :  0.048   0.246   1563
  Planarity :  0.007   0.163   1689
  Dihedral  : 11.305 131.389   1464
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 19.28
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.61 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.63 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.23), residues: 1197
  helix: -0.03 (0.19), residues: 679
  sheet:  0.66 (0.49), residues: 97
  loop : -2.26 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP D  92 
 HIS   0.021   0.002   HIS B 196 
 PHE   0.033   0.003   PHE B  66 
 TYR   0.027   0.002   TYR B  98 
 ARG   0.011   0.001   ARG C 154 

*********************** 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
  331 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 329
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.8600 (pmm) cc_final: 0.8324 (pmm)
REVERT: A   76 MET cc_start: 0.9348 (ptt) cc_final: 0.8669 (tmm)
REVERT: A   77 LEU cc_start: 0.9130 (mt) cc_final: 0.8656 (mt)
REVERT: A   79 LEU cc_start: 0.9069 (mm) cc_final: 0.8842 (mm)
REVERT: A   80 HIS cc_start: 0.7938 (m170) cc_final: 0.7169 (m170)
REVERT: A   98 TYR cc_start: 0.7524 (t80) cc_final: 0.7037 (t80)
REVERT: A  109 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8536 (ttpp)
REVERT: A  116 ARG cc_start: 0.8315 (mmt-90) cc_final: 0.7775 (mmp80)
REVERT: A  153 PHE cc_start: 0.9186 (t80) cc_final: 0.8959 (t80)
REVERT: A  179 HIS cc_start: 0.8492 (m-70) cc_final: 0.8061 (m-70)
REVERT: A  201 PHE cc_start: 0.8441 (m-80) cc_final: 0.8100 (m-80)
REVERT: A  204 MET cc_start: 0.8463 (tpp) cc_final: 0.7749 (tpp)
REVERT: A  210 ILE cc_start: 0.9275 (mm) cc_final: 0.9074 (mm)
REVERT: A  211 LYS cc_start: 0.9102 (mttt) cc_final: 0.8286 (mttt)
REVERT: A  349 GLU cc_start: 0.9404 (tp30) cc_final: 0.9104 (tp30)
REVERT: A  372 GLU cc_start: 0.9182 (mp0) cc_final: 0.8975 (mp0)
REVERT: A  373 LYS cc_start: 0.9713 (tmmt) cc_final: 0.9156 (mttt)
REVERT: A  376 LEU cc_start: 0.9704 (mm) cc_final: 0.9313 (mm)
REVERT: A  380 HIS cc_start: 0.9242 (m-70) cc_final: 0.8715 (m90)
REVERT: B   19 MET cc_start: 0.7646 (pmm) cc_final: 0.7004 (pmm)
REVERT: B   78 CYS cc_start: 0.8854 (p) cc_final: 0.8640 (p)
REVERT: B  174 ARG cc_start: 0.9231 (mtp180) cc_final: 0.9018 (ptp-170)
REVERT: B  189 THR cc_start: 0.7148 (p) cc_final: 0.6289 (p)
REVERT: B  192 GLN cc_start: 0.7463 (mt0) cc_final: 0.7214 (mp10)
REVERT: B  354 LEU cc_start: 0.9643 (mm) cc_final: 0.9297 (mm)
REVERT: B  363 LEU cc_start: 0.9335 (mt) cc_final: 0.9007 (mt)
REVERT: B  376 LEU cc_start: 0.9756 (mt) cc_final: 0.9353 (mt)
REVERT: B  380 HIS cc_start: 0.8988 (m90) cc_final: 0.8332 (m90)
REVERT: C   52 LYS cc_start: 0.6731 (mttm) cc_final: 0.6243 (mmmt)
REVERT: C   58 HIS cc_start: 0.9231 (m170) cc_final: 0.8989 (m170)
REVERT: C  159 LYS cc_start: 0.7953 (mttt) cc_final: 0.7698 (tptp)
REVERT: C  160 PHE cc_start: 0.8795 (t80) cc_final: 0.8143 (t80)
REVERT: C  163 LYS cc_start: 0.7487 (tttt) cc_final: 0.6683 (pttt)
REVERT: C  189 ILE cc_start: 0.8692 (mt) cc_final: 0.8379 (mm)
REVERT: C  200 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8013 (mt-10)
REVERT: C  213 LYS cc_start: 0.8677 (tttp) cc_final: 0.8344 (tttt)
REVERT: C  222 LEU cc_start: 0.9207 (pp) cc_final: 0.8850 (tt)
REVERT: D   46 GLU cc_start: 0.8596 (tt0) cc_final: 0.7622 (pm20)
REVERT: D  124 ASP cc_start: 0.9646 (m-30) cc_final: 0.9290 (m-30)
REVERT: D  126 LEU cc_start: 0.9810 (mt) cc_final: 0.9591 (mt)
REVERT: D  149 MET cc_start: 0.9131 (mpp) cc_final: 0.8691 (mpp)
REVERT: D  212 MET cc_start: 0.6531 (mtp) cc_final: 0.5995 (ptt)
  outliers start: 2
  outliers final: 0
  residues processed: 329
  average time/residue: 0.2317
  time to fit residues: 103.6904
Evaluate side-chains
  282 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 115 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 GLN
C 130 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.125991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.100979 restraints weight = 31576.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.104272 restraints weight = 21446.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.106810 restraints weight = 15834.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.6394

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= 0.232
  Angle     :  0.807  12.558  13514  Z= 0.436
  Chirality :  0.047   0.256   1563
  Planarity :  0.007   0.157   1689
  Dihedral  : 10.931 125.561   1464
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.36 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.49 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.24), residues: 1197
  helix: -0.09 (0.19), residues: 694
  sheet:  0.50 (0.49), residues: 100
  loop : -2.20 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D  92 
 HIS   0.028   0.002   HIS B 196 
 PHE   0.037   0.002   PHE B  66 
 TYR   0.025   0.002   TYR B  98 
 ARG   0.005   0.001   ARG D  95 

*********************** 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
  337 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 336
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.8600 (pmm) cc_final: 0.8256 (pmm)
REVERT: A   76 MET cc_start: 0.9272 (ptt) cc_final: 0.8519 (tmm)
REVERT: A   77 LEU cc_start: 0.9127 (mt) cc_final: 0.8650 (mt)
REVERT: A   80 HIS cc_start: 0.7841 (m170) cc_final: 0.7208 (m170)
REVERT: A   98 TYR cc_start: 0.7700 (t80) cc_final: 0.7319 (t80)
REVERT: A  109 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8448 (ttpp)
REVERT: A  116 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7683 (mmp80)
REVERT: A  132 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8197 (mtm180)
REVERT: A  153 PHE cc_start: 0.9159 (t80) cc_final: 0.8786 (t80)
REVERT: A  179 HIS cc_start: 0.8310 (m-70) cc_final: 0.7866 (m-70)
REVERT: A  204 MET cc_start: 0.8415 (tpp) cc_final: 0.7749 (tpp)
REVERT: A  211 LYS cc_start: 0.9163 (mttt) cc_final: 0.8545 (mttt)
REVERT: A  248 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8580 (ttpt)
REVERT: A  252 ASP cc_start: 0.9291 (m-30) cc_final: 0.9054 (m-30)
REVERT: A  259 GLU cc_start: 0.7649 (pm20) cc_final: 0.7257 (pm20)
REVERT: A  327 HIS cc_start: 0.7574 (m-70) cc_final: 0.5854 (m-70)
REVERT: A  370 ASP cc_start: 0.8871 (t70) cc_final: 0.8650 (t70)
REVERT: A  372 GLU cc_start: 0.9136 (mp0) cc_final: 0.8880 (mp0)
REVERT: A  373 LYS cc_start: 0.9701 (tmmt) cc_final: 0.9172 (mttt)
REVERT: A  377 MET cc_start: 0.9172 (tmm) cc_final: 0.8831 (tmm)
REVERT: B   19 MET cc_start: 0.8105 (pmm) cc_final: 0.7415 (pmm)
REVERT: B  137 MET cc_start: 0.8002 (tpt) cc_final: 0.7771 (tpp)
REVERT: B  187 TYR cc_start: 0.7344 (t80) cc_final: 0.6646 (t80)
REVERT: B  189 THR cc_start: 0.6642 (p) cc_final: 0.5736 (p)
REVERT: B  309 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8426 (mt-10)
REVERT: B  354 LEU cc_start: 0.9641 (mm) cc_final: 0.9290 (mm)
REVERT: B  355 GLN cc_start: 0.9467 (mt0) cc_final: 0.8921 (mt0)
REVERT: B  363 LEU cc_start: 0.9363 (mt) cc_final: 0.8975 (mt)
REVERT: B  366 LEU cc_start: 0.7769 (tp) cc_final: 0.6972 (tt)
REVERT: B  376 LEU cc_start: 0.9700 (mt) cc_final: 0.9285 (mt)
REVERT: B  377 MET cc_start: 0.9555 (ttm) cc_final: 0.9318 (ttm)
REVERT: B  380 HIS cc_start: 0.8983 (m90) cc_final: 0.8540 (m-70)
REVERT: C   58 HIS cc_start: 0.9220 (m170) cc_final: 0.9007 (m170)
REVERT: C   76 PHE cc_start: 0.9132 (m-80) cc_final: 0.8837 (m-80)
REVERT: C  159 LYS cc_start: 0.7873 (mttt) cc_final: 0.7626 (tptp)
REVERT: C  160 PHE cc_start: 0.8755 (t80) cc_final: 0.8454 (t80)
REVERT: C  191 THR cc_start: 0.9049 (m) cc_final: 0.8505 (p)
REVERT: C  197 PHE cc_start: 0.8912 (m-80) cc_final: 0.8657 (t80)
REVERT: C  200 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7860 (mt-10)
REVERT: C  213 LYS cc_start: 0.8530 (tttp) cc_final: 0.8225 (tttt)
REVERT: C  222 LEU cc_start: 0.9199 (pp) cc_final: 0.8980 (tt)
REVERT: D  115 LEU cc_start: 0.9129 (mp) cc_final: 0.8406 (tt)
REVERT: D  124 ASP cc_start: 0.9644 (m-30) cc_final: 0.9291 (m-30)
REVERT: D  148 LYS cc_start: 0.9236 (ptpp) cc_final: 0.8988 (ptpp)
REVERT: D  149 MET cc_start: 0.9078 (mpp) cc_final: 0.8492 (mpp)
REVERT: D  212 MET cc_start: 0.5658 (mtp) cc_final: 0.5437 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 336
  average time/residue: 0.2364
  time to fit residues: 107.9950
Evaluate side-chains
  282 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 GLN
C 109 GLN
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.123698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.099456 restraints weight = 31669.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.102763 restraints weight = 21014.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.105189 restraints weight = 15255.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.6808

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= 0.247
  Angle     :  0.816  12.132  13514  Z= 0.440
  Chirality :  0.046   0.252   1563
  Planarity :  0.007   0.155   1689
  Dihedral  : 10.922 119.313   1464
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  9.52 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  4.17 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.24), residues: 1197
  helix: -0.15 (0.19), residues: 688
  sheet:  0.53 (0.50), residues: 102
  loop : -2.34 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  92 
 HIS   0.037   0.002   HIS B 196 
 PHE   0.037   0.003   PHE B  66 
 TYR   0.026   0.002   TYR B  98 
 ARG   0.005   0.001   ARG D  95 

*********************** 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
  337 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 333
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.8727 (pmm) cc_final: 0.8334 (pmm)
REVERT: A   44 TYR cc_start: 0.5650 (m-80) cc_final: 0.5408 (m-80)
REVERT: A   76 MET cc_start: 0.9283 (ptt) cc_final: 0.8511 (tmm)
REVERT: A   77 LEU cc_start: 0.9005 (mt) cc_final: 0.8642 (mt)
REVERT: A   80 HIS cc_start: 0.7802 (m170) cc_final: 0.7230 (m170)
REVERT: A  109 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8472 (ttpp)
REVERT: A  116 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7582 (mmp80)
REVERT: A  118 GLU cc_start: 0.8883 (pt0) cc_final: 0.8555 (pt0)
REVERT: A  132 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8007 (mtm180)
REVERT: A  153 PHE cc_start: 0.9165 (t80) cc_final: 0.8576 (t80)
REVERT: A  179 HIS cc_start: 0.8233 (m-70) cc_final: 0.7879 (m-70)
REVERT: A  204 MET cc_start: 0.8468 (tpp) cc_final: 0.7794 (tpp)
REVERT: A  211 LYS cc_start: 0.9070 (mttt) cc_final: 0.8522 (mttt)
REVERT: A  213 LEU cc_start: 0.8915 (tt) cc_final: 0.8661 (tt)
REVERT: A  244 LEU cc_start: 0.5502 (mt) cc_final: 0.5247 (mm)
REVERT: A  248 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8648 (mttp)
REVERT: A  253 HIS cc_start: 0.7882 (m90) cc_final: 0.7501 (m90)
REVERT: A  327 HIS cc_start: 0.7538 (m-70) cc_final: 0.5850 (m-70)
REVERT: A  351 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8708 (tm-30)
REVERT: A  362 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9133 (pp20)
REVERT: A  370 ASP cc_start: 0.8876 (t70) cc_final: 0.8604 (t70)
REVERT: A  372 GLU cc_start: 0.9090 (mp0) cc_final: 0.8861 (mp0)
REVERT: A  373 LYS cc_start: 0.9719 (tmmt) cc_final: 0.9172 (mttt)
REVERT: A  376 LEU cc_start: 0.9715 (mm) cc_final: 0.9404 (mm)
REVERT: A  377 MET cc_start: 0.9212 (tmm) cc_final: 0.8859 (tmm)
REVERT: A  380 HIS cc_start: 0.9293 (m-70) cc_final: 0.8780 (m-70)
REVERT: B   19 MET cc_start: 0.8194 (pmm) cc_final: 0.7534 (pmm)
REVERT: B   54 GLN cc_start: 0.9623 (pp30) cc_final: 0.9419 (pp30)
REVERT: B   57 ILE cc_start: 0.8946 (tt) cc_final: 0.8723 (tt)
REVERT: B   88 LYS cc_start: 0.9450 (tttt) cc_final: 0.9077 (tptp)
REVERT: B  137 MET cc_start: 0.8141 (tpt) cc_final: 0.7935 (tpp)
REVERT: B  187 TYR cc_start: 0.8224 (t80) cc_final: 0.7582 (t80)
REVERT: B  192 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6842 (mp10)
REVERT: B  196 HIS cc_start: 0.8257 (m-70) cc_final: 0.7885 (m-70)
REVERT: B  198 MET cc_start: 0.8807 (mmp) cc_final: 0.8353 (mmt)
REVERT: B  307 ASN cc_start: 0.8211 (m110) cc_final: 0.7583 (t0)
REVERT: B  309 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8442 (mt-10)
REVERT: B  354 LEU cc_start: 0.9627 (mm) cc_final: 0.9293 (mm)
REVERT: B  363 LEU cc_start: 0.9329 (mt) cc_final: 0.8944 (mt)
REVERT: B  376 LEU cc_start: 0.9715 (mt) cc_final: 0.9230 (mt)
REVERT: B  380 HIS cc_start: 0.8968 (m90) cc_final: 0.8624 (m90)
REVERT: B  400 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9140 (mm-30)
REVERT: C   42 TRP cc_start: 0.8600 (t60) cc_final: 0.7924 (t60)
REVERT: C   48 ASP cc_start: 0.8258 (p0) cc_final: 0.7954 (p0)
REVERT: C   76 PHE cc_start: 0.9119 (m-80) cc_final: 0.8808 (m-80)
REVERT: C  160 PHE cc_start: 0.8803 (t80) cc_final: 0.8317 (t80)
REVERT: C  163 LYS cc_start: 0.7320 (tttt) cc_final: 0.6557 (pttt)
REVERT: C  191 THR cc_start: 0.9262 (m) cc_final: 0.8590 (p)
REVERT: C  198 LEU cc_start: 0.9231 (tp) cc_final: 0.9014 (tp)
REVERT: C  200 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8438 (mt-10)
REVERT: C  231 THR cc_start: 0.8005 (t) cc_final: 0.7781 (t)
REVERT: D  115 LEU cc_start: 0.9129 (mp) cc_final: 0.8420 (tt)
REVERT: D  124 ASP cc_start: 0.9629 (m-30) cc_final: 0.9277 (m-30)
REVERT: D  148 LYS cc_start: 0.9242 (ptpp) cc_final: 0.9018 (ptpp)
REVERT: D  149 MET cc_start: 0.8979 (mpp) cc_final: 0.8352 (mpp)
REVERT: D  212 MET cc_start: 0.5316 (mtp) cc_final: 0.5061 (mtp)
  outliers start: 4
  outliers final: 0
  residues processed: 337
  average time/residue: 0.2272
  time to fit residues: 104.5034
Evaluate side-chains
  278 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 276
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 113 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 95 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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**
B 335 ASN
C 103 GLN
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.126808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.101989 restraints weight = 31656.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.105301 restraints weight = 21175.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.107800 restraints weight = 15477.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.7243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   9970  Z= 0.228
  Angle     :  0.833  12.241  13514  Z= 0.449
  Chirality :  0.047   0.265   1563
  Planarity :  0.007   0.154   1689
  Dihedral  : 10.770 120.145   1464
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.94 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.24), residues: 1197
  helix: -0.24 (0.19), residues: 694
  sheet:  0.69 (0.52), residues: 102
  loop : -2.14 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  92 
 HIS   0.032   0.002   HIS B 196 
 PHE   0.034   0.002   PHE A 201 
 TYR   0.024   0.002   TYR B  98 
 ARG   0.010   0.001   ARG A 240 

*********************** 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
  335 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 1.030 
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: A   19 MET cc_start: 0.8734 (pmm) cc_final: 0.8336 (pmm)
REVERT: A   76 MET cc_start: 0.9268 (ptt) cc_final: 0.8527 (tmm)
REVERT: A   77 LEU cc_start: 0.8983 (mt) cc_final: 0.8599 (mt)
REVERT: A   80 HIS cc_start: 0.7673 (m170) cc_final: 0.7090 (m170)
REVERT: A  109 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8486 (ttpp)
REVERT: A  132 ARG cc_start: 0.8424 (mtm110) cc_final: 0.8138 (mtm180)
REVERT: A  153 PHE cc_start: 0.9189 (t80) cc_final: 0.8821 (t80)
REVERT: A  174 ARG cc_start: 0.9228 (mtp180) cc_final: 0.8920 (mtp180)
REVERT: A  204 MET cc_start: 0.8417 (tpp) cc_final: 0.7699 (tpp)
REVERT: A  211 LYS cc_start: 0.9018 (mttt) cc_final: 0.8300 (mttt)
REVERT: A  213 LEU cc_start: 0.8836 (tt) cc_final: 0.8566 (tt)
REVERT: A  248 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8536 (tppt)
REVERT: A  253 HIS cc_start: 0.7914 (m90) cc_final: 0.7555 (m90)
REVERT: A  327 HIS cc_start: 0.7430 (m-70) cc_final: 0.5806 (m-70)
REVERT: A  370 ASP cc_start: 0.8886 (t70) cc_final: 0.8664 (t70)
REVERT: A  372 GLU cc_start: 0.8850 (mp0) cc_final: 0.8559 (mp0)
REVERT: A  376 LEU cc_start: 0.9714 (mm) cc_final: 0.9457 (mm)
REVERT: A  377 MET cc_start: 0.9172 (tmm) cc_final: 0.8861 (tmm)
REVERT: A  380 HIS cc_start: 0.9328 (m-70) cc_final: 0.8788 (m-70)
REVERT: B   19 MET cc_start: 0.8264 (pmm) cc_final: 0.7128 (pmm)
REVERT: B   57 ILE cc_start: 0.8887 (tt) cc_final: 0.8658 (tt)
REVERT: B   88 LYS cc_start: 0.9452 (tttt) cc_final: 0.9086 (tptp)
REVERT: B  110 LYS cc_start: 0.9394 (mmpt) cc_final: 0.9070 (tppt)
REVERT: B  179 HIS cc_start: 0.8639 (m-70) cc_final: 0.8373 (m-70)
REVERT: B  187 TYR cc_start: 0.7843 (t80) cc_final: 0.7499 (t80)
REVERT: B  196 HIS cc_start: 0.7934 (m-70) cc_final: 0.7565 (m-70)
REVERT: B  198 MET cc_start: 0.8655 (mmp) cc_final: 0.8206 (mmt)
REVERT: B  307 ASN cc_start: 0.8374 (m110) cc_final: 0.7848 (t0)
REVERT: B  309 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: B  354 LEU cc_start: 0.9651 (mm) cc_final: 0.9316 (mm)
REVERT: B  363 LEU cc_start: 0.9352 (mt) cc_final: 0.8964 (mt)
REVERT: B  370 ASP cc_start: 0.8669 (t0) cc_final: 0.8295 (p0)
REVERT: B  376 LEU cc_start: 0.9711 (mt) cc_final: 0.9191 (mt)
REVERT: B  380 HIS cc_start: 0.9069 (m90) cc_final: 0.8696 (m90)
REVERT: B  397 LEU cc_start: 0.9526 (mt) cc_final: 0.9270 (mt)
REVERT: B  400 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9134 (mm-30)
REVERT: C   88 GLU cc_start: 0.8841 (tp30) cc_final: 0.8487 (tp30)
REVERT: C   91 LEU cc_start: 0.9056 (tp) cc_final: 0.8666 (tp)
REVERT: C  212 MET cc_start: 0.7291 (mmm) cc_final: 0.7053 (mmm)
REVERT: D  106 LEU cc_start: 0.9387 (mt) cc_final: 0.9186 (mp)
REVERT: D  115 LEU cc_start: 0.9059 (mp) cc_final: 0.8314 (tt)
REVERT: D  124 ASP cc_start: 0.9648 (m-30) cc_final: 0.9304 (m-30)
REVERT: D  149 MET cc_start: 0.8863 (mpp) cc_final: 0.7957 (mpp)
REVERT: D  157 ILE cc_start: 0.9287 (mt) cc_final: 0.8603 (mt)
REVERT: D  212 MET cc_start: 0.5204 (mtp) cc_final: 0.4967 (mtp)
REVERT: D  219 PHE cc_start: 0.7268 (p90) cc_final: 0.6967 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 335
  average time/residue: 0.2275
  time to fit residues: 104.3977
Evaluate side-chains
  278 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 86 optimal weight:    0.0370
   chunk 24 optimal weight:    0.1980
   chunk 91 optimal weight:    0.6980
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.5460

-------------------------------------------------------------------------------
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**
B 392 ASN
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 202 GLN
C 210 ASN
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.128639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.103226 restraints weight = 32042.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.106549 restraints weight = 21584.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.109106 restraints weight = 15866.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.7669

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= 0.234
  Angle     :  0.838  12.383  13514  Z= 0.450
  Chirality :  0.047   0.274   1563
  Planarity :  0.007   0.153   1689
  Dihedral  : 10.637 121.061   1464
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.85 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.24), residues: 1197
  helix: -0.28 (0.19), residues: 688
  sheet:  0.77 (0.52), residues: 101
  loop : -2.22 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 191 
 HIS   0.028   0.001   HIS B 196 
 PHE   0.042   0.002   PHE B  66 
 TYR   0.023   0.002   TYR B  98 
 ARG   0.015   0.001   ARG B 398 

*********************** 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
  339 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 339
  time to evaluate  : 1.159 
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: 0.8732 (pmm) cc_final: 0.8313 (pmm)
REVERT: A   44 TYR cc_start: 0.5418 (m-80) cc_final: 0.5148 (m-80)
REVERT: A   54 GLN cc_start: 0.9247 (mt0) cc_final: 0.9026 (mm-40)
REVERT: A   76 MET cc_start: 0.9289 (ptt) cc_final: 0.8516 (tmm)
REVERT: A   77 LEU cc_start: 0.9023 (mt) cc_final: 0.8630 (mt)
REVERT: A   80 HIS cc_start: 0.7678 (m170) cc_final: 0.7143 (m170)
REVERT: A  109 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8407 (ttpp)
REVERT: A  132 ARG cc_start: 0.8416 (mtm110) cc_final: 0.8154 (mtm180)
REVERT: A  153 PHE cc_start: 0.9107 (t80) cc_final: 0.8696 (t80)
REVERT: A  174 ARG cc_start: 0.9206 (mtp180) cc_final: 0.8951 (mtp180)
REVERT: A  179 HIS cc_start: 0.8370 (m-70) cc_final: 0.8083 (m-70)
REVERT: A  200 ILE cc_start: 0.9453 (tp) cc_final: 0.9161 (tt)
REVERT: A  204 MET cc_start: 0.8374 (tpp) cc_final: 0.7713 (tpp)
REVERT: A  211 LYS cc_start: 0.8969 (mttt) cc_final: 0.8223 (mttt)
REVERT: A  213 LEU cc_start: 0.8831 (tt) cc_final: 0.8561 (tt)
REVERT: A  217 GLN cc_start: 0.9404 (mp10) cc_final: 0.9134 (mp10)
REVERT: A  248 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8587 (tppt)
REVERT: A  252 ASP cc_start: 0.9329 (m-30) cc_final: 0.9127 (m-30)
REVERT: A  253 HIS cc_start: 0.7983 (m90) cc_final: 0.7602 (m90)
REVERT: A  327 HIS cc_start: 0.7500 (m-70) cc_final: 0.5787 (m-70)
REVERT: A  359 GLU cc_start: 0.9421 (pm20) cc_final: 0.9210 (pm20)
REVERT: A  376 LEU cc_start: 0.9699 (mm) cc_final: 0.9318 (mm)
REVERT: A  377 MET cc_start: 0.9184 (tmm) cc_final: 0.8858 (tmm)
REVERT: A  380 HIS cc_start: 0.9312 (m-70) cc_final: 0.8626 (m90)
REVERT: B   20 ASP cc_start: 0.8137 (m-30) cc_final: 0.7414 (m-30)
REVERT: B   45 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8762 (tm-30)
REVERT: B   55 LEU cc_start: 0.9066 (mt) cc_final: 0.8851 (mt)
REVERT: B   66 PHE cc_start: 0.7317 (t80) cc_final: 0.7069 (t80)
REVERT: B   88 LYS cc_start: 0.9473 (tttt) cc_final: 0.9067 (tptp)
REVERT: B  110 LYS cc_start: 0.9415 (mmpt) cc_final: 0.8961 (tptp)
REVERT: B  179 HIS cc_start: 0.8565 (m-70) cc_final: 0.8338 (m-70)
REVERT: B  187 TYR cc_start: 0.7666 (t80) cc_final: 0.7381 (t80)
REVERT: B  196 HIS cc_start: 0.8119 (m-70) cc_final: 0.7807 (m-70)
REVERT: B  198 MET cc_start: 0.8476 (mmp) cc_final: 0.7948 (mmt)
REVERT: B  307 ASN cc_start: 0.8055 (m110) cc_final: 0.7590 (t0)
REVERT: B  309 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8243 (mt-10)
REVERT: B  354 LEU cc_start: 0.9617 (mm) cc_final: 0.9207 (mm)
REVERT: B  363 LEU cc_start: 0.9355 (mt) cc_final: 0.8926 (mt)
REVERT: B  376 LEU cc_start: 0.9691 (mt) cc_final: 0.9149 (mt)
REVERT: B  377 MET cc_start: 0.9519 (ttm) cc_final: 0.8825 (tmm)
REVERT: B  380 HIS cc_start: 0.9006 (m90) cc_final: 0.8669 (m90)
REVERT: B  386 ILE cc_start: 0.9407 (tp) cc_final: 0.9170 (tp)
REVERT: B  390 GLN cc_start: 0.9442 (pt0) cc_final: 0.9189 (pt0)
REVERT: B  400 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9130 (mm-30)
REVERT: C   86 THR cc_start: 0.8407 (m) cc_final: 0.7593 (p)
REVERT: C   88 GLU cc_start: 0.8882 (tp30) cc_final: 0.8524 (tp30)
REVERT: C   91 LEU cc_start: 0.9154 (tp) cc_final: 0.8684 (tp)
REVERT: C  160 PHE cc_start: 0.8708 (t80) cc_final: 0.8254 (t80)
REVERT: C  163 LYS cc_start: 0.7329 (tttt) cc_final: 0.6798 (pttt)
REVERT: C  218 LYS cc_start: 0.7511 (mppt) cc_final: 0.5912 (mppt)
REVERT: D  106 LEU cc_start: 0.9275 (mt) cc_final: 0.9045 (mp)
REVERT: D  115 LEU cc_start: 0.9053 (mp) cc_final: 0.8321 (tt)
REVERT: D  124 ASP cc_start: 0.9646 (m-30) cc_final: 0.9297 (m-30)
REVERT: D  149 MET cc_start: 0.8609 (mpp) cc_final: 0.8023 (mpp)
REVERT: D  181 ILE cc_start: 0.7251 (mm) cc_final: 0.6984 (mm)
REVERT: D  212 MET cc_start: 0.5302 (mtp) cc_final: 0.4954 (mtp)
REVERT: D  219 PHE cc_start: 0.7070 (p90) cc_final: 0.6773 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 339
  average time/residue: 0.2390
  time to fit residues: 110.7202
Evaluate side-chains
  281 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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**
** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.128794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.102976 restraints weight = 32121.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.106258 restraints weight = 22014.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.108714 restraints weight = 16386.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.7922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   9970  Z= 0.233
  Angle     :  0.842  14.090  13514  Z= 0.451
  Chirality :  0.048   0.263   1563
  Planarity :  0.006   0.153   1689
  Dihedral  : 10.592 122.850   1464
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.27 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.34 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.24), residues: 1197
  helix: -0.27 (0.19), residues: 688
  sheet:  0.93 (0.56), residues: 96
  loop : -2.13 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 191 
 HIS   0.025   0.001   HIS B 196 
 PHE   0.046   0.002   PHE B  66 
 TYR   0.019   0.002   TYR B  98 
 ARG   0.007   0.001   ARG C  95 

*********************** 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
  327 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 1.073 
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: 0.8788 (pmm) cc_final: 0.8384 (pmm)
REVERT: A   44 TYR cc_start: 0.5389 (m-80) cc_final: 0.5035 (m-80)
REVERT: A   54 GLN cc_start: 0.9257 (mt0) cc_final: 0.9030 (mm-40)
REVERT: A   76 MET cc_start: 0.9270 (ptt) cc_final: 0.8444 (tmm)
REVERT: A   77 LEU cc_start: 0.9012 (mt) cc_final: 0.8523 (mt)
REVERT: A   80 HIS cc_start: 0.7533 (m170) cc_final: 0.6962 (m170)
REVERT: A  109 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8403 (ttpp)
REVERT: A  132 ARG cc_start: 0.8386 (mtm110) cc_final: 0.8042 (mtm180)
REVERT: A  153 PHE cc_start: 0.9100 (t80) cc_final: 0.8763 (t80)
REVERT: A  200 ILE cc_start: 0.9484 (tp) cc_final: 0.9226 (tt)
REVERT: A  204 MET cc_start: 0.8495 (tpp) cc_final: 0.7834 (tpp)
REVERT: A  211 LYS cc_start: 0.8984 (mttt) cc_final: 0.8284 (mttt)
REVERT: A  213 LEU cc_start: 0.8795 (tt) cc_final: 0.8529 (tt)
REVERT: A  217 GLN cc_start: 0.9392 (mp10) cc_final: 0.9153 (mp10)
REVERT: A  248 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8582 (tppt)
REVERT: A  253 HIS cc_start: 0.8025 (m90) cc_final: 0.7621 (m90)
REVERT: A  327 HIS cc_start: 0.7519 (m-70) cc_final: 0.5820 (m-70)
REVERT: A  370 ASP cc_start: 0.9187 (p0) cc_final: 0.8660 (p0)
REVERT: A  373 LYS cc_start: 0.9677 (pptt) cc_final: 0.9407 (pptt)
REVERT: A  377 MET cc_start: 0.9085 (tmm) cc_final: 0.8867 (tmm)
REVERT: B   20 ASP cc_start: 0.8186 (m-30) cc_final: 0.7959 (m-30)
REVERT: B   55 LEU cc_start: 0.9067 (mt) cc_final: 0.8846 (mt)
REVERT: B   88 LYS cc_start: 0.9478 (tttt) cc_final: 0.8884 (tptp)
REVERT: B   91 LEU cc_start: 0.9224 (tp) cc_final: 0.8831 (pp)
REVERT: B  110 LYS cc_start: 0.9439 (mmpt) cc_final: 0.9069 (tppt)
REVERT: B  179 HIS cc_start: 0.8472 (m-70) cc_final: 0.8208 (m-70)
REVERT: B  187 TYR cc_start: 0.7782 (t80) cc_final: 0.7498 (t80)
REVERT: B  196 HIS cc_start: 0.8169 (m-70) cc_final: 0.7773 (m-70)
REVERT: B  198 MET cc_start: 0.8495 (mmp) cc_final: 0.8090 (mmt)
REVERT: B  307 ASN cc_start: 0.8060 (m110) cc_final: 0.7574 (t0)
REVERT: B  309 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8248 (mt-10)
REVERT: B  355 GLN cc_start: 0.9454 (tt0) cc_final: 0.9017 (pp30)
REVERT: B  363 LEU cc_start: 0.9368 (mt) cc_final: 0.8925 (mt)
REVERT: B  376 LEU cc_start: 0.9674 (mt) cc_final: 0.9098 (mt)
REVERT: B  377 MET cc_start: 0.9531 (ttm) cc_final: 0.8840 (tmm)
REVERT: B  380 HIS cc_start: 0.9014 (m90) cc_final: 0.8680 (m90)
REVERT: B  386 ILE cc_start: 0.9386 (tp) cc_final: 0.9153 (tp)
REVERT: B  390 GLN cc_start: 0.9446 (pt0) cc_final: 0.9184 (pt0)
REVERT: B  400 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9158 (mm-30)
REVERT: C   88 GLU cc_start: 0.8948 (tp30) cc_final: 0.8568 (tp30)
REVERT: C   91 LEU cc_start: 0.9095 (tp) cc_final: 0.8633 (tp)
REVERT: C  160 PHE cc_start: 0.8688 (t80) cc_final: 0.8309 (t80)
REVERT: C  163 LYS cc_start: 0.7161 (tttt) cc_final: 0.6669 (pttt)
REVERT: C  212 MET cc_start: 0.6945 (mmm) cc_final: 0.6451 (mmm)
REVERT: D  106 LEU cc_start: 0.9317 (mt) cc_final: 0.9079 (mp)
REVERT: D  124 ASP cc_start: 0.9668 (m-30) cc_final: 0.9350 (m-30)
REVERT: D  147 LEU cc_start: 0.8512 (mt) cc_final: 0.8229 (mt)
REVERT: D  149 MET cc_start: 0.9044 (mpp) cc_final: 0.8410 (mpp)
REVERT: D  209 MET cc_start: 0.1035 (ppp) cc_final: -0.0520 (mmt)
REVERT: D  212 MET cc_start: 0.4958 (mtp) cc_final: 0.4703 (mtp)
REVERT: D  219 PHE cc_start: 0.7057 (p90) cc_final: 0.6763 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.2274
  time to fit residues: 102.5249
Evaluate side-chains
  284 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   chunk 106 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 115 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0570
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.3904

-------------------------------------------------------------------------------
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**
** 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.127849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.102023 restraints weight = 31669.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.105301 restraints weight = 21708.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.107668 restraints weight = 16162.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.8044

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= 0.239
  Angle     :  0.846  11.009  13514  Z= 0.459
  Chirality :  0.048   0.259   1563
  Planarity :  0.007   0.154   1689
  Dihedral  : 10.569 123.758   1464
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  8.27 %
    Favored  : 91.40 %
  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 : 6.06 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.24), residues: 1197
  helix: -0.33 (0.19), residues: 689
  sheet:  1.05 (0.56), residues: 98
  loop : -2.15 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 191 
 HIS   0.023   0.001   HIS B 196 
 PHE   0.033   0.002   PHE B  66 
 TYR   0.019   0.002   TYR B  98 
 ARG   0.011   0.001   ARG C  59 

********************** 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
  329 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 329
  time to evaluate  : 1.064 
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: 0.8816 (pmm) cc_final: 0.8393 (pmm)
REVERT: A   44 TYR cc_start: 0.5406 (m-80) cc_final: 0.5159 (m-80)
REVERT: A   54 GLN cc_start: 0.9277 (mt0) cc_final: 0.9054 (mm-40)
REVERT: A   76 MET cc_start: 0.9302 (ptt) cc_final: 0.8511 (tmm)
REVERT: A   77 LEU cc_start: 0.8997 (mt) cc_final: 0.8547 (mt)
REVERT: A   80 HIS cc_start: 0.7546 (m170) cc_final: 0.7055 (m170)
REVERT: A  109 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8432 (ttpp)
REVERT: A  132 ARG cc_start: 0.8363 (mtm110) cc_final: 0.8016 (mtm180)
REVERT: A  153 PHE cc_start: 0.9127 (t80) cc_final: 0.8129 (t80)
REVERT: A  200 ILE cc_start: 0.9493 (tp) cc_final: 0.9055 (tt)
REVERT: A  204 MET cc_start: 0.8586 (tpp) cc_final: 0.8094 (tpp)
REVERT: A  211 LYS cc_start: 0.8957 (mttt) cc_final: 0.8380 (mttt)
REVERT: A  213 LEU cc_start: 0.8854 (tt) cc_final: 0.8584 (tt)
REVERT: A  217 GLN cc_start: 0.9401 (mp10) cc_final: 0.9146 (mp10)
REVERT: A  253 HIS cc_start: 0.7959 (m90) cc_final: 0.7482 (m90)
REVERT: A  327 HIS cc_start: 0.7548 (m-70) cc_final: 0.5812 (m-70)
REVERT: A  373 LYS cc_start: 0.9662 (pptt) cc_final: 0.9381 (pptt)
REVERT: B   55 LEU cc_start: 0.9053 (mt) cc_final: 0.8840 (mt)
REVERT: B   88 LYS cc_start: 0.9489 (tttt) cc_final: 0.8914 (tptp)
REVERT: B   91 LEU cc_start: 0.9250 (tp) cc_final: 0.8851 (pp)
REVERT: B  110 LYS cc_start: 0.9453 (mmpt) cc_final: 0.9074 (tppt)
REVERT: B  157 PHE cc_start: 0.8705 (m-10) cc_final: 0.8432 (m-10)
REVERT: B  187 TYR cc_start: 0.7913 (t80) cc_final: 0.7577 (t80)
REVERT: B  198 MET cc_start: 0.8566 (mmp) cc_final: 0.7971 (mmp)
REVERT: B  307 ASN cc_start: 0.8174 (m110) cc_final: 0.7593 (t0)
REVERT: B  309 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8311 (mt-10)
REVERT: B  340 TYR cc_start: 0.9132 (m-10) cc_final: 0.8806 (m-80)
REVERT: B  355 GLN cc_start: 0.9359 (tt0) cc_final: 0.9060 (pp30)
REVERT: B  363 LEU cc_start: 0.9359 (mt) cc_final: 0.8950 (mt)
REVERT: B  376 LEU cc_start: 0.9686 (mt) cc_final: 0.9083 (mt)
REVERT: B  380 HIS cc_start: 0.8917 (m90) cc_final: 0.8533 (m90)
REVERT: B  400 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9165 (mm-30)
REVERT: C   59 ARG cc_start: 0.8959 (mmm160) cc_final: 0.8713 (mmm-85)
REVERT: C   78 HIS cc_start: 0.8998 (p-80) cc_final: 0.8793 (p-80)
REVERT: C   86 THR cc_start: 0.8400 (p) cc_final: 0.7780 (p)
REVERT: C   88 GLU cc_start: 0.9091 (tp30) cc_final: 0.8713 (tp30)
REVERT: C  163 LYS cc_start: 0.7368 (tttt) cc_final: 0.6880 (pttt)
REVERT: C  212 MET cc_start: 0.6991 (mmm) cc_final: 0.6491 (mmm)
REVERT: C  218 LYS cc_start: 0.7662 (mppt) cc_final: 0.6387 (mppt)
REVERT: D  113 GLU cc_start: 0.8698 (tp30) cc_final: 0.8446 (tp30)
REVERT: D  115 LEU cc_start: 0.9152 (mp) cc_final: 0.8460 (tt)
REVERT: D  124 ASP cc_start: 0.9655 (m-30) cc_final: 0.9327 (m-30)
REVERT: D  140 ARG cc_start: 0.8170 (ptm160) cc_final: 0.7708 (ptp90)
REVERT: D  149 MET cc_start: 0.9103 (mpp) cc_final: 0.8520 (mpp)
REVERT: D  209 MET cc_start: 0.1260 (ppp) cc_final: -0.0380 (mmt)
REVERT: D  219 PHE cc_start: 0.7239 (p90) cc_final: 0.6956 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 329
  average time/residue: 0.2215
  time to fit residues: 100.1281
Evaluate side-chains
  285 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 117 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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**
B  22 HIS
** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 186 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.130052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.103904 restraints weight = 31670.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.107161 restraints weight = 21886.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.109560 restraints weight = 16394.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.8308

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= 0.231
  Angle     :  0.863  20.494  13514  Z= 0.459
  Chirality :  0.048   0.262   1563
  Planarity :  0.006   0.153   1689
  Dihedral  : 10.454 123.807   1464
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  8.52 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.24), residues: 1197
  helix: -0.41 (0.19), residues: 699
  sheet:  1.06 (0.56), residues: 98
  loop : -2.26 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 191 
 HIS   0.011   0.001   HIS A 196 
 PHE   0.033   0.002   PHE B  66 
 TYR   0.025   0.002   TYR B 357 
 ARG   0.009   0.001   ARG C  59 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3348.68 seconds
wall clock time: 60 minutes 54.53 seconds (3654.53 seconds total)