Starting phenix.real_space_refine
on Mon Jan 20 15:21:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xfc_38301/01_2025/8xfc_38301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xfc_38301/01_2025/8xfc_38301.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xfc_38301/01_2025/8xfc_38301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xfc_38301/01_2025/8xfc_38301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xfc_38301/01_2025/8xfc_38301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xfc_38301/01_2025/8xfc_38301.cif"
  }
  resolution = 3.89
  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=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3593 atoms to isotropic.
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       6      5.49       5
     S      26      5.16       5
     C    7880      2.51       5
     N    2212      2.21       5
     O    2247      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 108 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12371
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2302
          Classifications: {'peptide': 308}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 292}
    Chain: "C"
      Number of atoms: 2133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2133
          Classifications: {'peptide': 284}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 270}
    Chain: "D"
      Number of atoms: 3913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 3913
          Classifications: {'peptide': 517}
          Link IDs: {'PTRANS': 26, 'TRANS': 490}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 3961
          Classifications: {'peptide': 517}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 41, 'TRANS': 475}
    Chain: "D"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 62
          Unusual residues: {'ATP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.15, per 1000 atoms: 0.42
  Number of scatterers: 12371
  At special positions: 0
  Unit cell: (92.66, 85.28, 170.56, 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      26     16.00
     P       6     15.00
     O    2247      8.00
     N    2212      7.00
     C    7880      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: 2.85
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2958

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 10 sheets defined
      51.7% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1 through 11
      removed outlier: 3.921A  pdb=" N   ARG B   7 " --> pdb=" O   TRP B   3 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA B  10 " --> pdb=" O   ALA B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 30
      removed outlier: 3.564A  pdb=" N   VAL B  27 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   PHE B  28 " --> pdb=" O   TYR B  24 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU B  30 " --> pdb=" O   MET B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 38
      removed outlier: 4.213A  pdb=" N   ALA B  37 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 61 through 75
    Processing helix  chain 'B' and resid 86 through 122
      removed outlier: 3.609A  pdb=" N   VAL B  90 " --> pdb=" O   PRO B  86 " (cutoff:3.500A)
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 126 through 142
      removed outlier: 3.552A  pdb=" N   ALA B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ILE B 142 " --> pdb=" O   VAL B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 157
    Processing helix  chain 'B' and resid 171 through 202
      removed outlier: 5.217A  pdb=" N   LEU B 177 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
      removed outlier: 4.732A  pdb=" N   MET B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   SER B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR B 189 " --> pdb=" O   MET B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 212
      removed outlier: 3.585A  pdb=" N   ARG B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 227
    Processing helix  chain 'B' and resid 229 through 245
      removed outlier: 4.187A  pdb=" N   VAL B 233 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 254
      removed outlier: 4.064A  pdb=" N   THR B 251 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 270
    Processing helix  chain 'B' and resid 273 through 302
      removed outlier: 4.336A  pdb=" N   SER B 278 " --> pdb=" O   PRO B 274 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ILE B 279 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 17
      removed outlier: 3.775A  pdb=" N   ASP C  10 " --> pdb=" O   GLY C   6 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TRP C  12 " --> pdb=" O   TRP C   8 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ARG C  13 " --> pdb=" O   LEU C   9 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ARG C  17 " --> pdb=" O   ARG C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 37
    Processing helix  chain 'C' and resid 38 through 41
    Processing helix  chain 'C' and resid 72 through 110
      removed outlier: 3.589A  pdb=" N   ARG C  76 " --> pdb=" O   ASP C  72 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   VAL C  78 " --> pdb=" O   TYR C  74 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   TYR C  79 " --> pdb=" O   SER C  75 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   GLY C  80 " --> pdb=" O   ARG C  76 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   ALA C  81 " --> pdb=" O   THR C  77 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   TYR C 109 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY C 110 " --> pdb=" O   ALA C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 126
    Processing helix  chain 'C' and resid 128 through 137
    Processing helix  chain 'C' and resid 144 through 172
      removed outlier: 3.513A  pdb=" N   VAL C 148 " --> pdb=" O   THR C 144 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE C 155 " --> pdb=" O   ILE C 151 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   TRP C 157 " --> pdb=" O   ALA C 153 " (cutoff:3.500A)
      Proline residue:  C 158  - end of helix
    Processing helix  chain 'C' and resid 175 through 182
      removed outlier: 3.590A  pdb=" N   LYS C 181 " --> pdb=" O   VAL C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 196
      removed outlier: 3.566A  pdb=" N   LEU C 191 " --> pdb=" O   ARG C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 225
      removed outlier: 4.515A  pdb=" N   VAL C 203 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C 204 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLY C 212 " --> pdb=" O   THR C 208 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU C 224 " --> pdb=" O   THR C 220 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLY C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 243
      removed outlier: 3.645A  pdb=" N   GLN C 243 " --> pdb=" O   ASN C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 279
      removed outlier: 3.892A  pdb=" N   ILE C 262 " --> pdb=" O   GLY C 258 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR C 263 " --> pdb=" O   ALA C 259 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL C 264 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU C 265 " --> pdb=" O   ALA C 261 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   MET C 270 " --> pdb=" O   ALA C 266 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA C 273 " --> pdb=" O   MET C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 284
      removed outlier: 3.757A  pdb=" N   ALA C 284 " --> pdb=" O   ALA C 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 54
    Processing helix  chain 'D' and resid 84 through 88
    Processing helix  chain 'D' and resid 110 through 116
      removed outlier: 3.582A  pdb=" N   GLU D 116 " --> pdb=" O   PHE D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 139
      removed outlier: 4.213A  pdb=" N   VAL D 132 " --> pdb=" O   ARG D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 147
    Processing helix  chain 'D' and resid 155 through 168
      removed outlier: 4.169A  pdb=" N   ARG D 161 " --> pdb=" O   GLY D 157 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 183
      removed outlier: 3.519A  pdb=" N   SER D 182 " --> pdb=" O   GLN D 179 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA D 183 " --> pdb=" O   PRO D 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 179 through 183'
    Processing helix  chain 'D' and resid 188 through 202
      removed outlier: 3.926A  pdb=" N   ASP D 201 " --> pdb=" O   GLN D 197 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   GLU D 202 " --> pdb=" O   GLY D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 221
    Processing helix  chain 'D' and resid 238 through 244
    Processing helix  chain 'D' and resid 247 through 256
    Processing helix  chain 'D' and resid 330 through 338
    Processing helix  chain 'D' and resid 362 through 368
    Processing helix  chain 'D' and resid 387 through 399
      removed outlier: 3.559A  pdb=" N   ILE D 392 " --> pdb=" O   VAL D 388 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU D 394 " --> pdb=" O   ARG D 390 " (cutoff:3.500A)
      Proline residue:  D 395  - end of helix
      removed outlier: 3.971A  pdb=" N   HIS D 399 " --> pdb=" O   PRO D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 418
      removed outlier: 3.956A  pdb=" N   ASP D 416 " --> pdb=" O   ARG D 412 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL D 418 " --> pdb=" O   LEU D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 421 through 425
      removed outlier: 4.101A  pdb=" N   LEU D 425 " --> pdb=" O   SER D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 428 through 432
    Processing helix  chain 'D' and resid 433 through 446
      removed outlier: 3.745A  pdb=" N   ARG D 437 " --> pdb=" O   SER D 433 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN D 438 " --> pdb=" O   GLY D 434 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 463 through 482
    Processing helix  chain 'D' and resid 516 through 521
    Processing helix  chain 'D' and resid 525 through 533
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 3.893A  pdb=" N   THR A  51 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 58
    Processing helix  chain 'A' and resid 109 through 121
      removed outlier: 3.694A  pdb=" N   PHE A 113 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 126
    Processing helix  chain 'A' and resid 128 through 134
      removed outlier: 4.610A  pdb=" N   HIS A 131 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 144
      removed outlier: 3.841A  pdb=" N   VAL A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 182
      removed outlier: 3.619A  pdb=" N   GLY A 181 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 4.013A  pdb=" N   PHE A 193 " --> pdb=" O   ASP A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 252 through 262
      removed outlier: 3.919A  pdb=" N   ALA A 256 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 284
    Processing helix  chain 'A' and resid 308 through 322
    Processing helix  chain 'A' and resid 324 through 332
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.757A  pdb=" N   VAL A 360 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 376
    Processing helix  chain 'A' and resid 395 through 407
    Processing helix  chain 'A' and resid 421 through 431
      removed outlier: 3.962A  pdb=" N   ILE A 429 " --> pdb=" O   PHE A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 454
      removed outlier: 3.649A  pdb=" N   PHE A 452 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 482
    Processing helix  chain 'A' and resid 485 through 501
      removed outlier: 3.627A  pdb=" N   SER A 489 " --> pdb=" O   THR A 485 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 18
      removed outlier: 3.555A  pdb=" N   THR D  17 " --> pdb=" O   ARG D  64 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG D  64 " --> pdb=" O   THR D  17 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'D' and resid 209 through 211
      removed outlier: 6.391A  pdb=" N   VAL D  38 " --> pdb=" O   LEU D 209 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   THR D 211 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   VAL D  40 " --> pdb=" O   THR D 211 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL D 224 " --> pdb=" O   SER D 235 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   SER D 235 " --> pdb=" O   VAL D 224 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL D 226 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'D' and resid 304 through 310
      removed outlier: 6.879A  pdb=" N   LYS D 289 " --> pdb=" O   ALA D 306 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ASP D 308 " --> pdb=" O   LEU D 287 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU D 287 " --> pdb=" O   ASP D 308 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL D 310 " --> pdb=" O   SER D 285 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   SER D 285 " --> pdb=" O   VAL D 310 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   GLU D 286 " --> pdb=" O   THR D 347 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   THR D 347 " --> pdb=" O   GLU D 286 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 488 through 489
      removed outlier: 8.351A  pdb=" N   SER D 489 " --> pdb=" O   LEU D 320 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ILE D 322 " --> pdb=" O   SER D 489 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU D 512 " --> pdb=" O   VAL D 504 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ARG D 506 " --> pdb=" O   VAL D 510 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   VAL D 510 " --> pdb=" O   ARG D 506 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 371 through 374
      removed outlier: 3.599A  pdb=" N   LEU D 453 " --> pdb=" O   THR D 484 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 36 through 39
      removed outlier: 6.586A  pdb=" N   VAL A  37 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 86
      removed outlier: 6.431A  pdb=" N   THR A  95 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   ILE A  84 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ARG A  93 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   SER A  86 " --> pdb=" O   ASN A  91 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ASN A  91 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASN A 161 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   THR A 166 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   VAL A 159 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339
      removed outlier: 3.663A  pdb=" N   SER A 338 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU A 298 " --> pdb=" O   PRO A 508 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP A 510 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   ILE A 294 " --> pdb=" O   TYR A 512 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   SER A 514 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ALA A 292 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   VAL A 516 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   GLY A 290 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ASN A 295 " --> pdb=" O   TRP A 442 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TRP A 442 " --> pdb=" O   ASN A 295 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 386 through 390
      removed outlier: 5.641A  pdb=" N   ILE A 387 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   GLN A 419 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   TYR A 389 " --> pdb=" O   GLN A 419 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    531 hydrogen bonds defined for protein.
    1527 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: 3.53

  Time building geometry restraints manager: 3.33 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: 2880
        1.33 -     1.45: 2541
        1.45 -     1.57: 7165
        1.57 -     1.69: 10
        1.69 -     1.81: 47
  Bond restraints: 12643
  Sorted by residual:
  bond pdb=" C4  ATP D 602 "
       pdb=" C5  ATP D 602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.469 -0.081 1.00e-02 1.00e+04 6.61e+01
  bond pdb=" C5  ATP D 602 "
       pdb=" C6  ATP D 602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.75e+01
  bond pdb=" C8  ATP D 602 "
       pdb=" N7  ATP D 602 "
    ideal  model  delta    sigma   weight residual
    1.310  1.357 -0.047 1.00e-02 1.00e+04 2.17e+01
  bond pdb=" C5  ATP D 602 "
       pdb=" N7  ATP D 602 "
    ideal  model  delta    sigma   weight residual
    1.387  1.343  0.044 1.00e-02 1.00e+04 1.93e+01
  bond pdb=" C4  ATP D 602 "
       pdb=" N9  ATP D 602 "
    ideal  model  delta    sigma   weight residual
    1.374  1.335  0.039 1.00e-02 1.00e+04 1.56e+01
  ... (remaining 12638 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.04: 17137
        4.04 -     8.09: 124
        8.09 -    12.13: 12
       12.13 -    16.18: 0
       16.18 -    20.22: 2
  Bond angle restraints: 17275
  Sorted by residual:
  angle pdb=" PB  ATP D 602 "
        pdb=" O3B ATP D 602 "
        pdb=" PG  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     139.87  119.65   20.22 1.00e+00 1.00e+00 4.09e+02
  angle pdb=" PA  ATP D 602 "
        pdb=" O3A ATP D 602 "
        pdb=" PB  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     136.83  120.20   16.63 1.00e+00 1.00e+00 2.77e+02
  angle pdb=" C5  ATP D 602 "
        pdb=" C4  ATP D 602 "
        pdb=" N3  ATP D 602 "
      ideal   model   delta    sigma   weight residual
     126.80  118.75    8.05 1.00e+00 1.00e+00 6.47e+01
  angle pdb=" C   ASP A 352 "
        pdb=" CA  ASP A 352 "
        pdb=" CB  ASP A 352 "
      ideal   model   delta    sigma   weight residual
     110.17  119.08   -8.91 1.11e+00 8.12e-01 6.44e+01
  angle pdb=" C   LEU A 348 "
        pdb=" CA  LEU A 348 "
        pdb=" CB  LEU A 348 "
      ideal   model   delta    sigma   weight residual
     109.85  118.72   -8.87 1.14e+00 7.69e-01 6.05e+01
  ... (remaining 17270 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 6760
       17.86 -    35.72: 603
       35.72 -    53.57: 119
       53.57 -    71.43: 32
       71.43 -    89.29: 10
  Dihedral angle restraints: 7524
    sinusoidal: 2901
      harmonic: 4623
  Sorted by residual:
  dihedral pdb=" C   SER A 262 "
           pdb=" N   SER A 262 "
           pdb=" CA  SER A 262 "
           pdb=" CB  SER A 262 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.43   14.83     0      2.50e+00 1.60e-01 3.52e+01
  dihedral pdb=" CA  LEU B 226 "
           pdb=" C   LEU B 226 "
           pdb=" N   ARG B 227 "
           pdb=" CA  ARG B 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.91   28.09     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  GLY C 237 "
           pdb=" C   GLY C 237 "
           pdb=" N   ASP C 238 "
           pdb=" CA  ASP C 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.90   27.10     0      5.00e+00 4.00e-02 2.94e+01
  ... (remaining 7521 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1952
       0.127 -    0.255: 48
       0.255 -    0.382: 4
       0.382 -    0.509: 4
       0.509 -    0.637: 2
  Chirality restraints: 2010
  Sorted by residual:
  chirality pdb=" CA  SER A 262 "
            pdb=" N   SER A 262 "
            pdb=" C   SER A 262 "
            pdb=" CB  SER A 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.87    0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" CA  ASN A 530 "
            pdb=" N   ASN A 530 "
            pdb=" C   ASN A 530 "
            pdb=" CB  ASN A 530 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.53 2.00e-01 2.50e+01 6.89e+00
  chirality pdb=" CA  ALA A 391 "
            pdb=" N   ALA A 391 "
            pdb=" C   ALA A 391 "
            pdb=" CB  ALA A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.01    0.47 2.00e-01 2.50e+01 5.53e+00
  ... (remaining 2007 not shown)

  Planarity restraints: 2240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 220 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   TRP A 220 "    0.042 2.00e-02 2.50e+03
        pdb=" O   TRP A 220 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLU A 221 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 490 "   -0.012 2.00e-02 2.50e+03   2.37e-02 5.63e+00
        pdb=" C   HIS A 490 "    0.041 2.00e-02 2.50e+03
        pdb=" O   HIS A 490 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU A 491 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 335 "    0.011 2.00e-02 2.50e+03   2.21e-02 4.89e+00
        pdb=" C   ARG D 335 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ARG D 335 "    0.014 2.00e-02 2.50e+03
        pdb=" N   MET D 336 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2237 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 217
        2.64 -     3.21: 12267
        3.21 -     3.77: 18491
        3.77 -     4.34: 24520
        4.34 -     4.90: 39872
  Nonbonded interactions: 95367
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 352 "
            pdb=" OD1 ASP A 352 "
     model   vdw
     2.081 3.120
  nonbonded pdb=" OG  SER C  52 "
            pdb=" OE1 GLN C  53 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" O   SER A 347 "
            pdb=" OG  SER A 347 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" O   GLU D  15 "
            pdb=" OG1 THR D  66 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER D 244 "
            pdb=" OE1 GLN D 246 "
     model   vdw
     2.224 3.040
  ... (remaining 95362 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             14.390
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     28.410
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
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      :  0.005   0.081  12643  Z= 0.337
  Angle     :  0.946  20.221  17275  Z= 0.618
  Chirality :  0.061   0.637   2010
  Planarity :  0.004   0.043   2240
  Dihedral  : 14.649  89.290   4566
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  9.03 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  5.83 %
    Favored  : 91.89 %
  Cbeta Deviations :  0.61 %
  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: -3.88 (0.18), residues: 1616
  helix: -1.61 (0.17), residues: 734
  sheet: -3.47 (0.40), residues: 112
  loop : -3.47 (0.19), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 112 
 HIS   0.005   0.001   HIS C  71 
 PHE   0.022   0.001   PHE B  95 
 TYR   0.008   0.001   TYR C  74 
 ARG   0.005   0.000   ARG D  86 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 1.455 
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: B  196 SER cc_start: 0.9315 (t) cc_final: 0.9095 (t)
REVERT: B  266 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8601 (tp40)
REVERT: C  218 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8631 (tm-30)
REVERT: C  269 MET cc_start: 0.8721 (ppp) cc_final: 0.8346 (tmm)
REVERT: C  270 MET cc_start: 0.9203 (tmm) cc_final: 0.8494 (tmm)
REVERT: D  101 MET cc_start: 0.8370 (mpp) cc_final: 0.8167 (mpp)
REVERT: D  486 LEU cc_start: 0.9153 (tt) cc_final: 0.8891 (tt)
REVERT: A  101 LYS cc_start: 0.9226 (mttp) cc_final: 0.9010 (mtpp)
REVERT: A  243 LYS cc_start: 0.9162 (tppt) cc_final: 0.8835 (tppt)
REVERT: A  268 LEU cc_start: 0.9114 (tp) cc_final: 0.8789 (tp)
REVERT: A  490 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8478 (m90)
  outliers start: 29
  outliers final: 16
  residues processed: 210
  average time/residue: 0.2907
  time to fit residues: 83.5927
Evaluate side-chains
  144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain D residue  316 ARG
Chi-restraints excluded: chain D residue  335 ARG
Chi-restraints excluded: chain D residue  497 GLN
Chi-restraints excluded: chain D residue  524 ARG
Chi-restraints excluded: chain A residue  149 LYS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  352 ASP
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  490 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    8.9990
   chunk 121 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0970
   chunk 125 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0770
   chunk 76 optimal weight:    3.9990
   chunk 93 optimal weight:    9.9990
   chunk 145 optimal weight:    7.9990
   overall best weight:    1.2340

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 GLN
B 201 ASN
B 228 ASN
B 256 ASN
C 138 GLN
C 142 HIS
D 105 ASN
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 478 GLN
A  82 GLN
A 125 ASN
A 131 HIS
A 223 ASN
A 264 ASN
A 330 GLN
A 331 GLN
A 404 ASN
A 408 ASN
A 431 ASN
** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 GLN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.064468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.055035 restraints weight = 55581.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.056656 restraints weight = 29809.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.057765 restraints weight = 19346.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12643  Z= 0.217
  Angle     :  0.674   9.396  17275  Z= 0.343
  Chirality :  0.044   0.176   2010
  Planarity :  0.004   0.046   2240
  Dihedral  :  9.196  85.992   1903
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.99 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  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: -2.58 (0.20), residues: 1616
  helix: -0.45 (0.19), residues: 743
  sheet: -2.90 (0.44), residues: 114
  loop : -2.87 (0.20), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 285 
 HIS   0.004   0.001   HIS C  71 
 PHE   0.012   0.001   PHE B 236 
 TYR   0.010   0.001   TYR C 176 
 ARG   0.006   0.000   ARG C 162 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 1.301 
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: B   24 TYR cc_start: 0.8576 (t80) cc_final: 0.8223 (t80)
REVERT: B  196 SER cc_start: 0.9308 (t) cc_final: 0.9096 (t)
REVERT: B  245 MET cc_start: 0.8672 (ptp) cc_final: 0.8384 (ptp)
REVERT: B  287 TYR cc_start: 0.8794 (t80) cc_final: 0.8585 (t80)
REVERT: C  269 MET cc_start: 0.8561 (ppp) cc_final: 0.8178 (tmm)
REVERT: C  270 MET cc_start: 0.9125 (tmm) cc_final: 0.8464 (tmm)
REVERT: D  316 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8361 (mmt90)
REVERT: D  486 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8990 (tt)
REVERT: A  268 LEU cc_start: 0.9204 (tp) cc_final: 0.8926 (tp)
  outliers start: 32
  outliers final: 21
  residues processed: 167
  average time/residue: 0.2462
  time to fit residues: 59.9796
Evaluate side-chains
  149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  213 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  316 ARG
Chi-restraints excluded: chain D residue  459 VAL
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  507 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 148 optimal weight:    5.9990
   chunk 112 optimal weight:    0.7980
   chunk 121 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 135 optimal weight:    0.9980
   chunk 127 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0870
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  53 GLN
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.065236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.055720 restraints weight = 55529.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.057377 restraints weight = 29350.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.058508 restraints weight = 18943.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12643  Z= 0.177
  Angle     :  0.635   9.745  17275  Z= 0.321
  Chirality :  0.043   0.172   2010
  Planarity :  0.004   0.045   2240
  Dihedral  :  7.942  77.838   1876
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.28 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  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: -2.01 (0.20), residues: 1616
  helix: -0.01 (0.19), residues: 748
  sheet: -2.39 (0.47), residues: 115
  loop : -2.60 (0.21), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 285 
 HIS   0.004   0.001   HIS A 490 
 PHE   0.012   0.001   PHE B  28 
 TYR   0.018   0.001   TYR B  69 
 ARG   0.006   0.000   ARG D 427 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 1.350 
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: B   24 TYR cc_start: 0.8499 (t80) cc_final: 0.8162 (t80)
REVERT: B   91 LEU cc_start: 0.9708 (mm) cc_final: 0.9398 (mt)
REVERT: B  109 GLU cc_start: 0.8858 (tt0) cc_final: 0.8450 (tt0)
REVERT: B  186 SER cc_start: 0.9121 (p) cc_final: 0.8541 (p)
REVERT: B  196 SER cc_start: 0.9228 (t) cc_final: 0.9020 (t)
REVERT: B  245 MET cc_start: 0.8617 (ptp) cc_final: 0.8337 (ptp)
REVERT: C  183 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8436 (pp)
REVERT: C  269 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8105 (tmm)
REVERT: C  270 MET cc_start: 0.9088 (tmm) cc_final: 0.8453 (tmm)
REVERT: D  486 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9040 (tt)
REVERT: A  268 LEU cc_start: 0.9138 (tp) cc_final: 0.8856 (tp)
REVERT: A  300 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.9018 (m)
REVERT: A  397 ASP cc_start: 0.9023 (p0) cc_final: 0.8782 (p0)
REVERT: A  511 ASP cc_start: 0.8516 (p0) cc_final: 0.8303 (p0)
  outliers start: 36
  outliers final: 20
  residues processed: 167
  average time/residue: 0.2382
  time to fit residues: 60.2074
Evaluate side-chains
  152 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  213 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 134 optimal weight:    0.0970
   chunk 111 optimal weight:    0.0050
   chunk 58 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 129 optimal weight:    0.9980
   chunk 120 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 72 optimal weight:    8.9990
   chunk 78 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 121 optimal weight:   10.0000
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 GLN
B 291 ASN
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.065869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.056458 restraints weight = 55146.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.058071 restraints weight = 29586.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.059200 restraints weight = 19414.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  12643  Z= 0.165
  Angle     :  0.629   9.838  17275  Z= 0.313
  Chirality :  0.043   0.164   2010
  Planarity :  0.004   0.051   2240
  Dihedral  :  7.338  75.045   1868
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.77 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  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: -1.63 (0.21), residues: 1616
  helix:  0.28 (0.19), residues: 747
  sheet: -1.97 (0.49), residues: 114
  loop : -2.41 (0.21), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 285 
 HIS   0.003   0.001   HIS C  71 
 PHE   0.010   0.001   PHE D 487 
 TYR   0.018   0.001   TYR B  69 
 ARG   0.007   0.000   ARG B  80 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 ARG cc_start: 0.8770 (tpt90) cc_final: 0.8449 (tpm170)
REVERT: B   24 TYR cc_start: 0.8435 (t80) cc_final: 0.8126 (t80)
REVERT: B   91 LEU cc_start: 0.9711 (mm) cc_final: 0.9406 (mt)
REVERT: B  109 GLU cc_start: 0.8812 (tt0) cc_final: 0.8484 (tt0)
REVERT: B  186 SER cc_start: 0.9037 (p) cc_final: 0.8600 (t)
REVERT: B  196 SER cc_start: 0.9203 (t) cc_final: 0.8983 (t)
REVERT: C  269 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8079 (tmm)
REVERT: C  270 MET cc_start: 0.9080 (tmm) cc_final: 0.8493 (tmm)
REVERT: D  486 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8969 (tt)
REVERT: A  196 MET cc_start: 0.8892 (mmm) cc_final: 0.8641 (mmt)
REVERT: A  268 LEU cc_start: 0.9100 (tp) cc_final: 0.8784 (tp)
REVERT: A  397 ASP cc_start: 0.9019 (p0) cc_final: 0.8761 (p0)
  outliers start: 29
  outliers final: 17
  residues processed: 163
  average time/residue: 0.2310
  time to fit residues: 56.1204
Evaluate side-chains
  145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 120 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 147 optimal weight:    8.9990
   chunk 64 optimal weight:    7.9990
   chunk 144 optimal weight:    6.9990
   chunk 81 optimal weight:    0.5980
   chunk 73 optimal weight:    8.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 ASN
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.063515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.054190 restraints weight = 56092.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.055749 restraints weight = 30209.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.056841 restraints weight = 19715.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12643  Z= 0.301
  Angle     :  0.669  10.490  17275  Z= 0.336
  Chirality :  0.044   0.173   2010
  Planarity :  0.004   0.057   2240
  Dihedral  :  7.048  72.520   1868
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 18.03 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  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: -1.52 (0.21), residues: 1616
  helix:  0.41 (0.20), residues: 748
  sheet: -2.18 (0.49), residues: 117
  loop : -2.35 (0.21), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 285 
 HIS   0.004   0.001   HIS A 235 
 PHE   0.019   0.001   PHE C 188 
 TYR   0.020   0.002   TYR D 354 
 ARG   0.006   0.000   ARG A 443 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 123
  time to evaluate  : 1.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8533 (tt)
REVERT: B  205 ASP cc_start: 0.8924 (m-30) cc_final: 0.8464 (t70)
REVERT: C  269 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8156 (tmm)
REVERT: C  270 MET cc_start: 0.9117 (tmm) cc_final: 0.8487 (tmm)
REVERT: D  486 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9079 (tt)
REVERT: A  268 LEU cc_start: 0.9275 (tp) cc_final: 0.8995 (tp)
REVERT: A  397 ASP cc_start: 0.9032 (p0) cc_final: 0.8800 (p0)
  outliers start: 44
  outliers final: 30
  residues processed: 151
  average time/residue: 0.2135
  time to fit residues: 49.5980
Evaluate side-chains
  150 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   16 PHE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  170 GLU
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 151 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 157 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 147 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 GLN
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.065271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.055754 restraints weight = 56423.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.057396 restraints weight = 30356.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.058484 restraints weight = 19733.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12643  Z= 0.178
  Angle     :  0.624  10.395  17275  Z= 0.309
  Chirality :  0.042   0.164   2010
  Planarity :  0.004   0.051   2240
  Dihedral  :  6.768  75.425   1868
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.84 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  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: -1.29 (0.21), residues: 1616
  helix:  0.57 (0.20), residues: 741
  sheet: -2.04 (0.50), residues: 117
  loop : -2.18 (0.22), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 112 
 HIS   0.003   0.001   HIS C  71 
 PHE   0.017   0.001   PHE C 188 
 TYR   0.019   0.001   TYR B  69 
 ARG   0.005   0.000   ARG C 162 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 LEU cc_start: 0.9716 (mm) cc_final: 0.9403 (mt)
REVERT: B  109 GLU cc_start: 0.8668 (tt0) cc_final: 0.8436 (tt0)
REVERT: B  186 SER cc_start: 0.9139 (p) cc_final: 0.8611 (t)
REVERT: C  183 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8441 (pp)
REVERT: C  269 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8019 (tmm)
REVERT: C  270 MET cc_start: 0.9091 (tmm) cc_final: 0.8466 (tmm)
REVERT: D  486 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9011 (tt)
REVERT: A  268 LEU cc_start: 0.9100 (tp) cc_final: 0.8795 (tp)
REVERT: A  397 ASP cc_start: 0.9013 (p0) cc_final: 0.8766 (p0)
  outliers start: 34
  outliers final: 23
  residues processed: 154
  average time/residue: 0.2213
  time to fit residues: 51.5712
Evaluate side-chains
  147 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue   69 GLN
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  349 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 106 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 131 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 153 optimal weight:    0.0670
   chunk 15 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.1324

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 GLN
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.065359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.055848 restraints weight = 56331.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.057444 restraints weight = 30348.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.058571 restraints weight = 19972.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12643  Z= 0.182
  Angle     :  0.635   9.892  17275  Z= 0.314
  Chirality :  0.043   0.176   2010
  Planarity :  0.004   0.050   2240
  Dihedral  :  6.516  77.745   1866
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.63 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  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: -1.22 (0.21), residues: 1616
  helix:  0.58 (0.20), residues: 747
  sheet: -1.97 (0.51), residues: 115
  loop : -2.10 (0.22), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 285 
 HIS   0.004   0.001   HIS C  71 
 PHE   0.015   0.001   PHE C 188 
 TYR   0.019   0.001   TYR B  69 
 ARG   0.005   0.000   ARG C 162 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8300 (pp30)
REVERT: B   91 LEU cc_start: 0.9715 (mm) cc_final: 0.9401 (mt)
REVERT: B  109 GLU cc_start: 0.8662 (tt0) cc_final: 0.8414 (tt0)
REVERT: B  186 SER cc_start: 0.9177 (p) cc_final: 0.8730 (t)
REVERT: C  183 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8453 (pp)
REVERT: C  269 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7853 (tmm)
REVERT: C  270 MET cc_start: 0.9073 (tmm) cc_final: 0.8434 (tmm)
REVERT: D  486 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9010 (tt)
REVERT: A  268 LEU cc_start: 0.9122 (tp) cc_final: 0.8838 (tp)
REVERT: A  397 ASP cc_start: 0.8992 (p0) cc_final: 0.8733 (p0)
  outliers start: 31
  outliers final: 23
  residues processed: 144
  average time/residue: 0.2264
  time to fit residues: 49.5381
Evaluate side-chains
  145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 GLN
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  349 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 121 optimal weight:    0.0970
   chunk 12 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 65 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 156 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    1.6182

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
B  55 HIS
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.064881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.055534 restraints weight = 56442.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.057126 restraints weight = 30299.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.058232 restraints weight = 19748.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12643  Z= 0.210
  Angle     :  0.647  11.325  17275  Z= 0.318
  Chirality :  0.043   0.173   2010
  Planarity :  0.004   0.063   2240
  Dihedral  :  6.341  80.872   1864
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.79 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  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: -1.25 (0.21), residues: 1616
  helix:  0.53 (0.20), residues: 757
  sheet: -1.95 (0.51), residues: 115
  loop : -2.14 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 285 
 HIS   0.006   0.001   HIS B  55 
 PHE   0.014   0.001   PHE C 188 
 TYR   0.018   0.001   TYR B  69 
 ARG   0.008   0.000   ARG C 162 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  109 GLU cc_start: 0.8689 (tt0) cc_final: 0.8460 (tt0)
REVERT: B  186 SER cc_start: 0.9222 (p) cc_final: 0.8755 (t)
REVERT: B  205 ASP cc_start: 0.8891 (m-30) cc_final: 0.8393 (t70)
REVERT: C  183 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8482 (pp)
REVERT: C  269 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7867 (tmm)
REVERT: C  270 MET cc_start: 0.9104 (tmm) cc_final: 0.8445 (tmm)
REVERT: D  486 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9020 (tt)
REVERT: A  268 LEU cc_start: 0.9161 (tp) cc_final: 0.8887 (tp)
REVERT: A  397 ASP cc_start: 0.9000 (p0) cc_final: 0.8745 (p0)
  outliers start: 33
  outliers final: 25
  residues processed: 141
  average time/residue: 0.2173
  time to fit residues: 47.3092
Evaluate side-chains
  146 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  349 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  539 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 153 optimal weight:    0.0970
   chunk 155 optimal weight:    5.9990
   chunk 136 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9980
   chunk 151 optimal weight:    0.9980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.065523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.055998 restraints weight = 56400.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.057645 restraints weight = 30387.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.058729 restraints weight = 19709.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12643  Z= 0.189
  Angle     :  0.661  12.512  17275  Z= 0.323
  Chirality :  0.043   0.173   2010
  Planarity :  0.004   0.048   2240
  Dihedral  :  6.226  85.317   1864
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.02 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  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: -1.14 (0.21), residues: 1616
  helix:  0.61 (0.20), residues: 755
  sheet: -1.60 (0.53), residues: 108
  loop : -2.10 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 285 
 HIS   0.003   0.001   HIS B  55 
 PHE   0.014   0.001   PHE C 188 
 TYR   0.020   0.001   TYR B  69 
 ARG   0.004   0.000   ARG B 304 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.8849 (ptp) cc_final: 0.8385 (pmm)
REVERT: B    8 ARG cc_start: 0.8822 (tpp-160) cc_final: 0.8620 (tpp-160)
REVERT: B   91 LEU cc_start: 0.9716 (mm) cc_final: 0.9403 (mt)
REVERT: B  109 GLU cc_start: 0.8718 (tt0) cc_final: 0.8506 (tt0)
REVERT: B  186 SER cc_start: 0.9243 (p) cc_final: 0.8783 (t)
REVERT: B  295 ASP cc_start: 0.8835 (t0) cc_final: 0.8505 (t0)
REVERT: C  183 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8496 (pp)
REVERT: C  269 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7980 (tmm)
REVERT: C  270 MET cc_start: 0.9069 (tmm) cc_final: 0.8463 (tmm)
REVERT: D  101 MET cc_start: 0.8457 (mpp) cc_final: 0.8202 (mpp)
REVERT: D  486 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9007 (tt)
REVERT: A  268 LEU cc_start: 0.9157 (tp) cc_final: 0.8889 (tp)
REVERT: A  397 ASP cc_start: 0.9017 (p0) cc_final: 0.8745 (p0)
  outliers start: 33
  outliers final: 26
  residues processed: 147
  average time/residue: 0.2188
  time to fit residues: 49.5233
Evaluate side-chains
  149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 GLN
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  349 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  285 ASP
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  539 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 140 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0070
   chunk 52 optimal weight:    5.9990
   chunk 131 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   chunk 57 optimal weight:    0.1980
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 150 optimal weight:    0.9990
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.066209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.056684 restraints weight = 55362.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.058350 restraints weight = 29849.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.059476 restraints weight = 19334.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12643  Z= 0.173
  Angle     :  0.680  12.970  17275  Z= 0.329
  Chirality :  0.043   0.176   2010
  Planarity :  0.004   0.075   2240
  Dihedral  :  6.105  88.480   1862
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.89 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  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: -1.05 (0.22), residues: 1616
  helix:  0.62 (0.20), residues: 760
  sheet: -1.50 (0.54), residues: 108
  loop : -2.02 (0.22), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 285 
 HIS   0.006   0.001   HIS B  55 
 PHE   0.014   0.001   PHE C 188 
 TYR   0.020   0.001   TYR B  69 
 ARG   0.008   0.000   ARG C 162 

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 1.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.8789 (ptp) cc_final: 0.8390 (pmm)
REVERT: B   91 LEU cc_start: 0.9701 (mm) cc_final: 0.9404 (mt)
REVERT: B  109 GLU cc_start: 0.8705 (tt0) cc_final: 0.8494 (tt0)
REVERT: B  186 SER cc_start: 0.9260 (p) cc_final: 0.8802 (t)
REVERT: B  295 ASP cc_start: 0.8841 (t0) cc_final: 0.8488 (t0)
REVERT: C  183 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: C  269 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7863 (tmm)
REVERT: C  270 MET cc_start: 0.9075 (tmm) cc_final: 0.8473 (tmm)
REVERT: D  101 MET cc_start: 0.8478 (mpp) cc_final: 0.8223 (mpp)
REVERT: D  486 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8974 (tt)
REVERT: A  268 LEU cc_start: 0.9125 (tp) cc_final: 0.8867 (tp)
REVERT: A  397 ASP cc_start: 0.8997 (p0) cc_final: 0.8729 (p0)
  outliers start: 28
  outliers final: 24
  residues processed: 147
  average time/residue: 0.2219
  time to fit residues: 49.8431
Evaluate side-chains
  148 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 GLN
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   63 TRP
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  349 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  539 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 156 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0050
   chunk 150 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.9996

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.066018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.056483 restraints weight = 56220.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.058138 restraints weight = 30358.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.059268 restraints weight = 19661.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12643  Z= 0.184
  Angle     :  0.670  12.994  17275  Z= 0.325
  Chirality :  0.043   0.179   2010
  Planarity :  0.004   0.047   2240
  Dihedral  :  6.033  88.806   1862
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.57 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  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: -1.05 (0.21), residues: 1616
  helix:  0.63 (0.20), residues: 758
  sheet: -1.49 (0.54), residues: 108
  loop : -2.03 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 285 
 HIS   0.004   0.001   HIS B  55 
 PHE   0.013   0.001   PHE D  72 
 TYR   0.019   0.001   TYR B  69 
 ARG   0.005   0.000   ARG B   8 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3243.39 seconds
wall clock time: 59 minutes 34.37 seconds (3574.37 seconds total)