Starting phenix.real_space_refine
on Wed Jul 30 05:59:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xjx_22216/07_2025/6xjx_22216_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xjx_22216/07_2025/6xjx_22216.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xjx_22216/07_2025/6xjx_22216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xjx_22216/07_2025/6xjx_22216.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xjx_22216/07_2025/6xjx_22216_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xjx_22216/07_2025/6xjx_22216_neut.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
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 12 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: 4
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    7808      2.51       5
     N    2039      2.21       5
     O    2162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12077
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1281
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 4, 'TRANS': 146}
    Chain: "B"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 389
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 3, 'TRANS': 46}
    Chain: "C"
      Number of atoms: 1281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1281
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 4, 'TRANS': 146}
    Chain: "D"
      Number of atoms: 400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 400
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 3, 'TRANS': 47}
    Chain: "E"
      Number of atoms: 1296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1296
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 5, 'TRANS': 147}
    Chain: "F"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 381
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 3, 'TRANS': 45}
    Chain: "G"
      Number of atoms: 1271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1271
          Classifications: {'peptide': 150}
          Link IDs: {'PTRANS': 4, 'TRANS': 145}
    Chain: "H"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 381
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 3, 'TRANS': 45}
    Chain: "Q"
      Number of atoms: 2972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2972
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 9, 'TRANS': 357}
    Chain: "R"
      Number of atoms: 2425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2425
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 3, 'TRANS': 287}
          Chain breaks: 1
  Time building chain proxies: 7.31, per 1000 atoms: 0.61
  Number of scatterers: 12077
  At special positions: 0
  Unit cell: (99.96, 128.282, 161.602, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      68     16.00
     O    2162      8.00
     N    2039      7.00
     C    7808      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: 2.79
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2778

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 3 sheets defined
      74.8% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 192 through 215
      removed outlier: 3.925A  pdb=" N   GLN A 196 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 256
      removed outlier: 4.404A  pdb=" N   ARG A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A 250 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 285
      removed outlier: 3.560A  pdb=" N   THR A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 311
    Processing helix  chain 'A' and resid 313 through 336
      removed outlier: 4.190A  pdb=" N   ASP A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 97
      removed outlier: 4.123A  pdb=" N   ILE B  75 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
      Proline residue:  B  76  - end of helix
    Processing helix  chain 'C' and resid 192 through 257
      removed outlier: 3.502A  pdb=" N   LEU C 214 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA C 215 " --> pdb=" O   LYS C 211 " (cutoff:3.500A)
      Proline residue:  C 216  - end of helix
      removed outlier: 4.295A  pdb=" N   LYS C 219 " --> pdb=" O   ALA C 215 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   VAL C 220 " --> pdb=" O   PRO C 216 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ARG C 221 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU C 250 " --> pdb=" O   GLN C 246 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   TRP C 255 " --> pdb=" O   ALA C 251 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   TRP C 256 " --> pdb=" O   ARG C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 284
      removed outlier: 3.592A  pdb=" N   ALA C 275 " --> pdb=" O   THR C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 311
      removed outlier: 4.189A  pdb=" N   ARG C 297 " --> pdb=" O   GLU C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 335
    Processing helix  chain 'D' and resid 65 through 72
    Processing helix  chain 'D' and resid 73 through 96
      removed outlier: 4.087A  pdb=" N   SER D  85 " --> pdb=" O   GLY D  81 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LYS D  86 " --> pdb=" O   THR D  82 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA D  90 " --> pdb=" O   LYS D  86 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   LEU D  91 " --> pdb=" O   ASN D  87 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ASP D  96 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 192 through 256
      Proline residue:  E 216  - end of helix
      removed outlier: 3.696A  pdb=" N   LYS E 219 " --> pdb=" O   ALA E 215 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL E 220 " --> pdb=" O   PRO E 216 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU E 240 " --> pdb=" O   LEU E 236 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE E 247 " --> pdb=" O   MET E 243 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE E 249 " --> pdb=" O   THR E 245 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   THR E 254 " --> pdb=" O   LEU E 250 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   TRP E 255 " --> pdb=" O   ALA E 251 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 259 through 285
      Proline residue:  E 265  - end of helix
      removed outlier: 3.719A  pdb=" N   ALA E 275 " --> pdb=" O   THR E 271 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE E 282 " --> pdb=" O   MET E 278 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 290 through 311
    Processing helix  chain 'E' and resid 313 through 335
      removed outlier: 3.540A  pdb=" N   ALA E 325 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 65 through 96
      Proline residue:  F  76  - end of helix
      removed outlier: 3.725A  pdb=" N   SER F  85 " --> pdb=" O   GLY F  81 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLU F  94 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 192 through 257
      removed outlier: 3.879A  pdb=" N   ARG G 201 " --> pdb=" O   LEU G 197 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA G 215 " --> pdb=" O   LYS G 211 " (cutoff:3.500A)
      Proline residue:  G 216  - end of helix
      removed outlier: 3.610A  pdb=" N   VAL G 220 " --> pdb=" O   PRO G 216 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLU G 223 " --> pdb=" O   LYS G 219 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU G 253 " --> pdb=" O   ILE G 249 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR G 254 " --> pdb=" O   LEU G 250 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   TRP G 255 " --> pdb=" O   ALA G 251 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 259 through 262
    Processing helix  chain 'G' and resid 263 through 286
      removed outlier: 3.973A  pdb=" N   THR G 271 " --> pdb=" O   THR G 267 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 290 through 310
      removed outlier: 4.179A  pdb=" N   GLY G 306 " --> pdb=" O   PHE G 302 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 313 through 340
      removed outlier: 3.601A  pdb=" N   GLN G 319 " --> pdb=" O   GLU G 315 " (cutoff:3.500A)
      Proline residue:  G 337  - end of helix
    Processing helix  chain 'H' and resid 65 through 96
      removed outlier: 4.027A  pdb=" N   ILE H  73 " --> pdb=" O   ARG H  69 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE H  75 " --> pdb=" O   PHE H  71 " (cutoff:3.500A)
      Proline residue:  H  76  - end of helix
      removed outlier: 3.506A  pdb=" N   LYS H  86 " --> pdb=" O   THR H  82 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 105 through 122
    Processing helix  chain 'Q' and resid 123 through 132
    Processing helix  chain 'Q' and resid 148 through 157
    Processing helix  chain 'Q' and resid 193 through 198
    Processing helix  chain 'Q' and resid 205 through 217
    Processing helix  chain 'Q' and resid 219 through 230
      removed outlier: 3.701A  pdb=" N   PHE Q 223 " --> pdb=" O   PRO Q 219 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE Q 230 " --> pdb=" O   ALA Q 226 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 239 through 251
    Processing helix  chain 'Q' and resid 268 through 281
    Processing helix  chain 'Q' and resid 292 through 314
    Processing helix  chain 'Q' and resid 315 through 316
      No H-bonds generated for 'chain 'Q' and resid 315 through 316'
    Processing helix  chain 'Q' and resid 317 through 321
    Processing helix  chain 'Q' and resid 323 through 332
    Processing helix  chain 'Q' and resid 338 through 350
    Processing helix  chain 'Q' and resid 360 through 375
      removed outlier: 3.870A  pdb=" N   VAL Q 364 " --> pdb=" O   THR Q 360 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LYS Q 372 " --> pdb=" O   PHE Q 368 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASN Q 373 " --> pdb=" O   THR Q 369 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ASN Q 375 " --> pdb=" O   LEU Q 371 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 377 through 387
      removed outlier: 3.718A  pdb=" N   MET Q 386 " --> pdb=" O   SER Q 382 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 392 through 404
    Processing helix  chain 'Q' and resid 409 through 421
      removed outlier: 3.741A  pdb=" N   CYS Q 413 " --> pdb=" O   SER Q 409 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 429 through 443
      removed outlier: 3.553A  pdb=" N   PHE Q 433 " --> pdb=" O   SER Q 429 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 451 through 469
      removed outlier: 4.044A  pdb=" N   ARG Q 455 " --> pdb=" O   MET Q 451 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 93
    Processing helix  chain 'R' and resid 105 through 115
    Processing helix  chain 'R' and resid 130 through 140
      removed outlier: 4.143A  pdb=" N   LEU R 136 " --> pdb=" O   ILE R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 153
    Processing helix  chain 'R' and resid 159 through 172
    Processing helix  chain 'R' and resid 177 through 184
      removed outlier: 3.551A  pdb=" N   PHE R 181 " --> pdb=" O   PHE R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 194 through 206
      removed outlier: 3.971A  pdb=" N   PHE R 198 " --> pdb=" O   LYS R 194 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LYS R 199 " --> pdb=" O   ARG R 195 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS R 202 " --> pdb=" O   PHE R 198 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ILE R 203 " --> pdb=" O   LYS R 199 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   SER R 205 " --> pdb=" O   GLN R 201 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS R 206 " --> pdb=" O   LYS R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 239
      removed outlier: 3.640A  pdb=" N   MET R 236 " --> pdb=" O   THR R 232 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   PHE R 239 " --> pdb=" O   GLN R 235 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 249 through 272
    Processing helix  chain 'R' and resid 279 through 288
    Processing helix  chain 'R' and resid 295 through 305
      removed outlier: 3.828A  pdb=" N   VAL R 303 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 314 through 327
      removed outlier: 3.672A  pdb=" N   PHE R 318 " --> pdb=" O   SER R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 328 through 338
    Processing helix  chain 'R' and resid 346 through 359
    Processing helix  chain 'R' and resid 364 through 374
    Processing helix  chain 'R' and resid 383 through 397
      removed outlier: 3.693A  pdb=" N   ARG R 397 " --> pdb=" O   ASN R 393 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'Q' and resid 134 through 138
    Processing sheet with id=AA2, first strand: chain 'R' and resid 101 through 103
    Processing sheet with id=AA3, first strand: chain 'R' and resid 191 through 192

    785 hydrogen bonds defined for protein.
    2331 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.98

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3727
        1.34 -     1.46: 2729
        1.46 -     1.58: 5759
        1.58 -     1.70: 0
        1.70 -     1.82: 124
  Bond restraints: 12339
  Sorted by residual:
  bond pdb=" CA  THR Q 265 "
       pdb=" C   THR Q 265 "
    ideal  model  delta    sigma   weight residual
    1.523  1.564 -0.040 1.34e-02 5.57e+03 9.10e+00
  bond pdb=" C   LYS Q 161 "
       pdb=" N   GLN Q 162 "
    ideal  model  delta    sigma   weight residual
    1.331  1.293  0.038 1.59e-02 3.96e+03 5.76e+00
  bond pdb=" CG1 ILE Q 210 "
       pdb=" CD1 ILE Q 210 "
    ideal  model  delta    sigma   weight residual
    1.513  1.421  0.092 3.90e-02 6.57e+02 5.57e+00
  bond pdb=" C   ARG Q 263 "
       pdb=" N   PRO Q 264 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 2.34e-02 1.83e+03 5.53e+00
  bond pdb=" CB  TRP C 255 "
       pdb=" CG  TRP C 255 "
    ideal  model  delta    sigma   weight residual
    1.498  1.428  0.070 3.10e-02 1.04e+03 5.12e+00
  ... (remaining 12334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 16083
        2.96 -     5.92: 424
        5.92 -     8.88: 64
        8.88 -    11.84: 14
       11.84 -    14.80: 2
  Bond angle restraints: 16587
  Sorted by residual:
  angle pdb=" C   VAL D  74 "
        pdb=" N   ILE D  75 "
        pdb=" CA  ILE D  75 "
      ideal   model   delta    sigma   weight residual
     120.33  124.77   -4.44 8.00e-01 1.56e+00 3.08e+01
  angle pdb=" CA  LEU Q 428 "
        pdb=" CB  LEU Q 428 "
        pdb=" CG  LEU Q 428 "
      ideal   model   delta    sigma   weight residual
     116.30  131.10  -14.80 3.50e+00 8.16e-02 1.79e+01
  angle pdb=" C   LEU R 362 "
        pdb=" N   SER R 363 "
        pdb=" CA  SER R 363 "
      ideal   model   delta    sigma   weight residual
     121.74  128.07   -6.33 1.58e+00 4.01e-01 1.61e+01
  angle pdb=" CA  LEU Q 270 "
        pdb=" CB  LEU Q 270 "
        pdb=" CG  LEU Q 270 "
      ideal   model   delta    sigma   weight residual
     116.30  130.22  -13.92 3.50e+00 8.16e-02 1.58e+01
  angle pdb=" N   ILE B  49 "
        pdb=" CA  ILE B  49 "
        pdb=" C   ILE B  49 "
      ideal   model   delta    sigma   weight residual
     113.42  108.97    4.45 1.17e+00 7.31e-01 1.44e+01
  ... (remaining 16582 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.91: 6742
       14.91 -    29.82: 519
       29.82 -    44.73: 151
       44.73 -    59.64: 14
       59.64 -    74.55: 13
  Dihedral angle restraints: 7439
    sinusoidal: 3151
      harmonic: 4288
  Sorted by residual:
  dihedral pdb=" CA  ARG A 335 "
           pdb=" C   ARG A 335 "
           pdb=" N   ASP A 336 "
           pdb=" CA  ASP A 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.45  -33.55     0      5.00e+00 4.00e-02 4.50e+01
  dihedral pdb=" CA  MET B  63 "
           pdb=" C   MET B  63 "
           pdb=" N   SER B  64 "
           pdb=" CA  SER B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.94   31.06     0      5.00e+00 4.00e-02 3.86e+01
  dihedral pdb=" CA  LEU C 253 "
           pdb=" C   LEU C 253 "
           pdb=" N   THR C 254 "
           pdb=" CA  THR C 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.20  -30.80     0      5.00e+00 4.00e-02 3.79e+01
  ... (remaining 7436 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1175
       0.054 -    0.108: 476
       0.108 -    0.162: 123
       0.162 -    0.216: 15
       0.216 -    0.270: 4
  Chirality restraints: 1793
  Sorted by residual:
  chirality pdb=" CB  ILE D  97 "
            pdb=" CA  ILE D  97 "
            pdb=" CG1 ILE D  97 "
            pdb=" CG2 ILE D  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  THR A 267 "
            pdb=" CA  THR A 267 "
            pdb=" OG1 THR A 267 "
            pdb=" CG2 THR A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  TYR C 291 "
            pdb=" N   TYR C 291 "
            pdb=" C   TYR C 291 "
            pdb=" CB  TYR C 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1790 not shown)

  Planarity restraints: 2094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP Q 231 "    0.014 2.00e-02 2.50e+03   2.71e-02 7.33e+00
        pdb=" C   ASP Q 231 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ASP Q 231 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU Q 232 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN Q 162 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO Q 163 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO Q 163 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO Q 163 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 311 "    0.012 2.00e-02 2.50e+03   2.46e-02 6.03e+00
        pdb=" C   GLU R 311 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLU R 311 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER R 312 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2091 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 67
        2.48 -     3.09: 8417
        3.09 -     3.69: 19382
        3.69 -     4.30: 26357
        4.30 -     4.90: 41408
  Nonbonded interactions: 95631
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS Q 341 "
            pdb=" OE2 GLU Q 432 "
     model   vdw
     1.876 3.120
  nonbonded pdb=" OD1 ASP Q 392 "
            pdb=" OG1 THR Q 395 "
     model   vdw
     2.034 3.040
  nonbonded pdb=" NH2 ARG R 150 "
            pdb=" OE1 GLU R 265 "
     model   vdw
     2.108 3.120
  nonbonded pdb=" OD1 ASP Q 231 "
            pdb=" NH2 ARG R 352 "
     model   vdw
     2.124 3.120
  nonbonded pdb=" OE2 GLU C 200 "
            pdb=" NH2 ARG C 335 "
     model   vdw
     2.131 3.120
  ... (remaining 95626 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 191 through 340)
  selection = (chain 'C' and resid 191 through 340)
  selection = (chain 'E' and resid 191 through 340)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'B' and resid 48 through 96)
  selection = (chain 'D' and resid 48 through 96)
  selection = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     27.970
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
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      :  0.009   0.096  12339  Z= 0.406
  Angle     :  1.205  14.805  16587  Z= 0.647
  Chirality :  0.060   0.270   1793
  Planarity :  0.007   0.065   2094
  Dihedral  : 12.138  74.550   4661
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  6.01 %
    Favored  : 93.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.41 (0.18), residues: 1440
  helix: -1.84 (0.13), residues: 1028
  sheet: -4.78 (0.59), residues: 15
  loop : -2.85 (0.27), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.005   TRP A 255 
 HIS   0.014   0.003   HIS A 304 
 PHE   0.035   0.004   PHE H  77 
 TYR   0.031   0.004   TYR Q 114 
 ARG   0.015   0.002   ARG C 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12392 (  785)
  hydrogen bonds       : angle       6.41219 ( 2331)
  covalent geometry    : bond        0.00869 (12339)
  covalent geometry    : angle       1.20458 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 352
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 MET cc_start: 0.9170 (mmm) cc_final: 0.8950 (mmm)
REVERT: A  276 MET cc_start: 0.9118 (ttt) cc_final: 0.8798 (ttt)
REVERT: A  278 MET cc_start: 0.9006 (mtt) cc_final: 0.8636 (mtm)
REVERT: A  331 LEU cc_start: 0.8833 (mt) cc_final: 0.8417 (tp)
REVERT: A  335 ARG cc_start: 0.7848 (tmt170) cc_final: 0.7604 (tmt-80)
REVERT: B   80 VAL cc_start: 0.9151 (t) cc_final: 0.8854 (t)
REVERT: B   91 LEU cc_start: 0.8260 (tm) cc_final: 0.7595 (mp)
REVERT: C  243 MET cc_start: 0.9316 (mtm) cc_final: 0.8788 (mtm)
REVERT: C  246 GLN cc_start: 0.9130 (tm130) cc_final: 0.8572 (tm-30)
REVERT: C  262 ILE cc_start: 0.8892 (mt) cc_final: 0.8670 (tp)
REVERT: C  276 MET cc_start: 0.8561 (ttm) cc_final: 0.8335 (tmm)
REVERT: C  284 MET cc_start: 0.8303 (mtp) cc_final: 0.8044 (tmm)
REVERT: C  313 ASP cc_start: 0.8613 (m-30) cc_final: 0.8347 (t0)
REVERT: D   77 PHE cc_start: 0.8124 (m-80) cc_final: 0.7919 (m-10)
REVERT: D   79 TYR cc_start: 0.8902 (t80) cc_final: 0.8487 (t80)
REVERT: D   97 ILE cc_start: 0.7980 (mt) cc_final: 0.7175 (tt)
REVERT: E  202 GLU cc_start: 0.9413 (tt0) cc_final: 0.9190 (tm-30)
REVERT: E  221 ARG cc_start: 0.8320 (tmt170) cc_final: 0.7695 (tmm160)
REVERT: E  243 MET cc_start: 0.8061 (tpt) cc_final: 0.7375 (tpp)
REVERT: E  262 ILE cc_start: 0.9574 (mt) cc_final: 0.9218 (mt)
REVERT: E  263 MET cc_start: 0.8118 (mmt) cc_final: 0.7914 (mmm)
REVERT: E  296 ASP cc_start: 0.9053 (m-30) cc_final: 0.8652 (m-30)
REVERT: E  313 ASP cc_start: 0.9031 (m-30) cc_final: 0.8721 (p0)
REVERT: E  329 MET cc_start: 0.9020 (tpt) cc_final: 0.8586 (tpp)
REVERT: E  330 ASP cc_start: 0.9396 (t0) cc_final: 0.9074 (p0)
REVERT: F   67 LEU cc_start: 0.7105 (tt) cc_final: 0.6694 (mt)
REVERT: F   71 PHE cc_start: 0.8290 (m-80) cc_final: 0.8053 (m-80)
REVERT: G  243 MET cc_start: 0.8035 (mmm) cc_final: 0.7590 (mmm)
REVERT: G  276 MET cc_start: 0.8833 (mtm) cc_final: 0.8273 (mtp)
REVERT: G  287 GLN cc_start: 0.8502 (tt0) cc_final: 0.8288 (tm-30)
REVERT: G  316 LYS cc_start: 0.9159 (mtpm) cc_final: 0.8603 (mmmt)
REVERT: G  335 ARG cc_start: 0.8828 (mmt180) cc_final: 0.8325 (ptt90)
REVERT: H   52 ARG cc_start: 0.8196 (mmt180) cc_final: 0.7903 (mtt180)
REVERT: H   67 LEU cc_start: 0.8736 (tt) cc_final: 0.8394 (tt)
REVERT: H   92 LEU cc_start: 0.8189 (tp) cc_final: 0.7848 (pp)
REVERT: Q  114 TYR cc_start: 0.8839 (t80) cc_final: 0.7599 (t80)
REVERT: Q  204 ILE cc_start: 0.9235 (mt) cc_final: 0.9034 (tp)
REVERT: Q  208 ASP cc_start: 0.8582 (m-30) cc_final: 0.8317 (m-30)
REVERT: Q  213 THR cc_start: 0.9094 (m) cc_final: 0.8667 (p)
REVERT: Q  228 LYS cc_start: 0.9159 (mttt) cc_final: 0.8795 (mttm)
REVERT: Q  256 MET cc_start: 0.8325 (mmm) cc_final: 0.7999 (mmm)
REVERT: Q  300 GLN cc_start: 0.8838 (tt0) cc_final: 0.8132 (tm-30)
REVERT: Q  368 PHE cc_start: 0.9136 (m-10) cc_final: 0.8598 (m-80)
REVERT: Q  375 ASN cc_start: 0.8223 (m-40) cc_final: 0.7555 (p0)
REVERT: Q  386 MET cc_start: 0.8287 (mtt) cc_final: 0.7821 (ttt)
REVERT: Q  445 LEU cc_start: 0.8643 (tp) cc_final: 0.8339 (tp)
REVERT: R   91 MET cc_start: 0.8469 (mtp) cc_final: 0.8125 (mmm)
REVERT: R  191 MET cc_start: 0.6151 (mmm) cc_final: 0.5463 (mmm)
REVERT: R  278 MET cc_start: 0.7974 (mmm) cc_final: 0.7118 (tpp)
REVERT: R  299 TYR cc_start: 0.8140 (m-10) cc_final: 0.7609 (m-10)
REVERT: R  322 CYS cc_start: 0.8928 (m) cc_final: 0.8554 (m)
REVERT: R  335 MET cc_start: 0.9037 (mmt) cc_final: 0.8724 (mmp)
REVERT: R  365 ASN cc_start: 0.8314 (m-40) cc_final: 0.8100 (m-40)
REVERT: R  382 LEU cc_start: 0.8312 (tp) cc_final: 0.8032 (tp)
REVERT: R  396 HIS cc_start: 0.8940 (m-70) cc_final: 0.8730 (p-80)
  outliers start: 5
  outliers final: 1
  residues processed: 357
  average time/residue: 0.2875
  time to fit residues: 138.2659
Evaluate side-chains
  197 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    9.9990
   chunk 108 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 129 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
C 196 GLN
C 213 GLN
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 341 HIS
F  95 HIS
Q 116 ASN
Q 222 ASN
Q 260 HIS
Q 295 ASN
Q 352 HIS
Q 425 ASN
R 178 HIS
** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.057195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.043966 restraints weight = 76133.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.045364 restraints weight = 43802.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.046282 restraints weight = 29693.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12339  Z= 0.199
  Angle     :  0.728  10.662  16587  Z= 0.381
  Chirality :  0.042   0.152   1793
  Planarity :  0.005   0.047   2094
  Dihedral  :  5.994  27.132   1605
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.24 %
    Favored  : 96.61 %
  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: -1.27 (0.20), residues: 1440
  helix: -0.22 (0.15), residues: 1053
  sheet: -4.43 (0.79), residues: 17
  loop : -2.21 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 255 
 HIS   0.005   0.001   HIS Q 411 
 PHE   0.033   0.002   PHE Q 188 
 TYR   0.024   0.002   TYR E 268 
 ARG   0.006   0.001   ARG C 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04658 (  785)
  hydrogen bonds       : angle       4.77795 ( 2331)
  covalent geometry    : bond        0.00417 (12339)
  covalent geometry    : angle       0.72755 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 261
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.8993 (ttm) cc_final: 0.8620 (ttm)
REVERT: A  263 MET cc_start: 0.9206 (mmm) cc_final: 0.9001 (mmm)
REVERT: A  267 THR cc_start: 0.8720 (m) cc_final: 0.8500 (m)
REVERT: A  278 MET cc_start: 0.8931 (mtt) cc_final: 0.8635 (mtm)
REVERT: A  322 ASP cc_start: 0.9169 (m-30) cc_final: 0.8843 (m-30)
REVERT: A  331 LEU cc_start: 0.8848 (mt) cc_final: 0.8563 (tp)
REVERT: B   83 LEU cc_start: 0.9186 (mm) cc_final: 0.8707 (mp)
REVERT: B   91 LEU cc_start: 0.7954 (tt) cc_final: 0.7508 (mp)
REVERT: C  242 TYR cc_start: 0.9045 (t80) cc_final: 0.8806 (t80)
REVERT: C  243 MET cc_start: 0.9234 (mtm) cc_final: 0.8715 (mtm)
REVERT: C  245 THR cc_start: 0.9700 (m) cc_final: 0.9497 (p)
REVERT: C  246 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: C  276 MET cc_start: 0.9069 (ttm) cc_final: 0.8729 (ttm)
REVERT: C  284 MET cc_start: 0.8466 (mtp) cc_final: 0.7825 (tmm)
REVERT: D   79 TYR cc_start: 0.8878 (t80) cc_final: 0.8429 (t80)
REVERT: D   97 ILE cc_start: 0.8186 (mt) cc_final: 0.7554 (tt)
REVERT: E  202 GLU cc_start: 0.9457 (tt0) cc_final: 0.8585 (tm-30)
REVERT: E  205 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8297 (pp20)
REVERT: E  213 GLN cc_start: 0.9208 (tt0) cc_final: 0.8991 (tt0)
REVERT: E  262 ILE cc_start: 0.9572 (mt) cc_final: 0.9291 (mt)
REVERT: E  263 MET cc_start: 0.8327 (mmt) cc_final: 0.8042 (mmm)
REVERT: E  276 MET cc_start: 0.9243 (tpp) cc_final: 0.8614 (tpp)
REVERT: E  296 ASP cc_start: 0.9195 (m-30) cc_final: 0.8951 (m-30)
REVERT: E  313 ASP cc_start: 0.9288 (m-30) cc_final: 0.8994 (p0)
REVERT: E  322 ASP cc_start: 0.9494 (t70) cc_final: 0.9108 (p0)
REVERT: E  329 MET cc_start: 0.9017 (tpt) cc_final: 0.8792 (tpp)
REVERT: E  330 ASP cc_start: 0.9333 (t0) cc_final: 0.9109 (p0)
REVERT: F   71 PHE cc_start: 0.8179 (m-80) cc_final: 0.7947 (m-80)
REVERT: F   83 LEU cc_start: 0.8931 (tt) cc_final: 0.8665 (mt)
REVERT: G  213 GLN cc_start: 0.9393 (mt0) cc_final: 0.9115 (mt0)
REVERT: G  276 MET cc_start: 0.8932 (mtm) cc_final: 0.8241 (mtp)
REVERT: H   52 ARG cc_start: 0.8211 (mmt180) cc_final: 0.7879 (mtt180)
REVERT: H   67 LEU cc_start: 0.8516 (tt) cc_final: 0.8263 (pt)
REVERT: H   92 LEU cc_start: 0.7788 (tp) cc_final: 0.7577 (pp)
REVERT: Q  176 PHE cc_start: 0.8253 (m-80) cc_final: 0.7904 (m-10)
REVERT: Q  204 ILE cc_start: 0.9423 (mt) cc_final: 0.9108 (tp)
REVERT: Q  208 ASP cc_start: 0.8752 (m-30) cc_final: 0.8436 (m-30)
REVERT: Q  229 MET cc_start: 0.8268 (mmm) cc_final: 0.7725 (mmm)
REVERT: Q  245 GLN cc_start: 0.9144 (mt0) cc_final: 0.8910 (mt0)
REVERT: Q  256 MET cc_start: 0.8279 (mmm) cc_final: 0.7974 (mmm)
REVERT: Q  330 MET cc_start: 0.8594 (tmm) cc_final: 0.8085 (tmm)
REVERT: Q  368 PHE cc_start: 0.9037 (m-10) cc_final: 0.8767 (m-80)
REVERT: Q  386 MET cc_start: 0.8552 (mtt) cc_final: 0.8163 (ttt)
REVERT: R   91 MET cc_start: 0.8423 (mtp) cc_final: 0.8072 (mmt)
REVERT: R  118 MET cc_start: 0.4271 (mmm) cc_final: 0.3573 (mtm)
REVERT: R  256 MET cc_start: 0.7913 (mtp) cc_final: 0.7690 (mtp)
REVERT: R  278 MET cc_start: 0.7300 (mmm) cc_final: 0.6928 (mmt)
REVERT: R  299 TYR cc_start: 0.8331 (m-10) cc_final: 0.8081 (m-10)
REVERT: R  321 PHE cc_start: 0.9260 (t80) cc_final: 0.8906 (t80)
REVERT: R  322 CYS cc_start: 0.8974 (m) cc_final: 0.8753 (m)
REVERT: R  335 MET cc_start: 0.9130 (mmt) cc_final: 0.8889 (mmp)
REVERT: R  382 LEU cc_start: 0.8225 (tp) cc_final: 0.7913 (tp)
REVERT: R  387 PHE cc_start: 0.9011 (t80) cc_final: 0.8782 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 263
  average time/residue: 0.2265
  time to fit residues: 86.5451
Evaluate side-chains
  192 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 106 optimal weight:   20.0000
   chunk 76 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 108 optimal weight:    9.9990
   chunk 59 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 339 GLN
D  87 ASN
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 260 HIS
Q 373 ASN
R 178 HIS
R 384 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.055988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.042685 restraints weight = 76467.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.044097 restraints weight = 43261.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.045005 restraints weight = 29039.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12339  Z= 0.244
  Angle     :  0.731   8.935  16587  Z= 0.385
  Chirality :  0.043   0.179   1793
  Planarity :  0.004   0.047   2094
  Dihedral  :  5.688  25.318   1605
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  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: -0.47 (0.21), residues: 1440
  helix:  0.39 (0.15), residues: 1055
  sheet: -4.55 (0.70), residues: 17
  loop : -1.97 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 256 
 HIS   0.006   0.002   HIS D  95 
 PHE   0.019   0.002   PHE R 197 
 TYR   0.023   0.002   TYR E 268 
 ARG   0.008   0.001   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04483 (  785)
  hydrogen bonds       : angle       4.65355 ( 2331)
  covalent geometry    : bond        0.00507 (12339)
  covalent geometry    : angle       0.73139 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 1.310 
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: A  263 MET cc_start: 0.9449 (mmm) cc_final: 0.9209 (mmm)
REVERT: A  267 THR cc_start: 0.8613 (m) cc_final: 0.8370 (m)
REVERT: A  322 ASP cc_start: 0.8939 (m-30) cc_final: 0.8600 (m-30)
REVERT: A  331 LEU cc_start: 0.8847 (mt) cc_final: 0.8600 (tp)
REVERT: B   83 LEU cc_start: 0.9103 (mm) cc_final: 0.8818 (mm)
REVERT: B   91 LEU cc_start: 0.7988 (tt) cc_final: 0.7623 (mp)
REVERT: C  243 MET cc_start: 0.9319 (mtm) cc_final: 0.8904 (ttp)
REVERT: C  246 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: C  276 MET cc_start: 0.9040 (ttm) cc_final: 0.8572 (tmm)
REVERT: C  284 MET cc_start: 0.8619 (mtp) cc_final: 0.7900 (tmm)
REVERT: D   79 TYR cc_start: 0.8855 (t80) cc_final: 0.8397 (t80)
REVERT: D   97 ILE cc_start: 0.7898 (mt) cc_final: 0.7230 (tt)
REVERT: E  202 GLU cc_start: 0.9419 (tt0) cc_final: 0.8711 (tm-30)
REVERT: E  205 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8234 (pp20)
REVERT: E  213 GLN cc_start: 0.9219 (tt0) cc_final: 0.9015 (tt0)
REVERT: E  243 MET cc_start: 0.8318 (tpp) cc_final: 0.8108 (ttt)
REVERT: E  246 GLN cc_start: 0.9248 (tt0) cc_final: 0.8888 (tm-30)
REVERT: E  262 ILE cc_start: 0.9584 (mt) cc_final: 0.9349 (mt)
REVERT: E  263 MET cc_start: 0.8399 (mmt) cc_final: 0.8088 (mmm)
REVERT: E  276 MET cc_start: 0.9270 (tpp) cc_final: 0.8898 (tpp)
REVERT: E  311 ARG cc_start: 0.8851 (mtm180) cc_final: 0.8405 (mtm-85)
REVERT: E  313 ASP cc_start: 0.9240 (m-30) cc_final: 0.9025 (p0)
REVERT: E  322 ASP cc_start: 0.9504 (t70) cc_final: 0.9121 (p0)
REVERT: E  329 MET cc_start: 0.9044 (tpt) cc_final: 0.8746 (tpp)
REVERT: E  330 ASP cc_start: 0.9336 (t0) cc_final: 0.9091 (p0)
REVERT: F   63 MET cc_start: 0.7519 (ttt) cc_final: 0.7301 (ttt)
REVERT: F   71 PHE cc_start: 0.8070 (m-80) cc_final: 0.7821 (m-80)
REVERT: F   83 LEU cc_start: 0.9160 (tt) cc_final: 0.8886 (mt)
REVERT: G  213 GLN cc_start: 0.9448 (mt0) cc_final: 0.9174 (mt0)
REVERT: G  243 MET cc_start: 0.8749 (mtp) cc_final: 0.8325 (mtp)
REVERT: G  276 MET cc_start: 0.9076 (mtm) cc_final: 0.8698 (tmm)
REVERT: G  278 MET cc_start: 0.8094 (mmt) cc_final: 0.7848 (mmm)
REVERT: G  335 ARG cc_start: 0.8688 (mmt180) cc_final: 0.8375 (ptt90)
REVERT: H   52 ARG cc_start: 0.8208 (mmt180) cc_final: 0.7985 (mtt180)
REVERT: H   67 LEU cc_start: 0.8318 (tt) cc_final: 0.8011 (pt)
REVERT: H   92 LEU cc_start: 0.7766 (tp) cc_final: 0.7534 (pp)
REVERT: Q  147 MET cc_start: 0.7977 (ptp) cc_final: 0.7529 (ptp)
REVERT: Q  176 PHE cc_start: 0.8104 (m-80) cc_final: 0.7511 (m-10)
REVERT: Q  208 ASP cc_start: 0.8845 (m-30) cc_final: 0.8606 (m-30)
REVERT: Q  229 MET cc_start: 0.8469 (mmm) cc_final: 0.8157 (mmm)
REVERT: Q  256 MET cc_start: 0.8434 (mmm) cc_final: 0.8058 (mmm)
REVERT: Q  330 MET cc_start: 0.8688 (tmm) cc_final: 0.8151 (tmm)
REVERT: Q  368 PHE cc_start: 0.9104 (m-10) cc_final: 0.8763 (m-80)
REVERT: Q  386 MET cc_start: 0.8500 (mtt) cc_final: 0.8193 (ttt)
REVERT: Q  445 LEU cc_start: 0.8570 (tp) cc_final: 0.8307 (tp)
REVERT: R   91 MET cc_start: 0.8435 (mtp) cc_final: 0.8051 (mmt)
REVERT: R  118 MET cc_start: 0.4541 (mmm) cc_final: 0.3990 (mtm)
REVERT: R  191 MET cc_start: 0.6696 (mmm) cc_final: 0.6091 (mmm)
REVERT: R  278 MET cc_start: 0.7538 (mmm) cc_final: 0.6169 (tpp)
REVERT: R  299 TYR cc_start: 0.8386 (m-10) cc_final: 0.8183 (m-10)
REVERT: R  321 PHE cc_start: 0.9135 (t80) cc_final: 0.8700 (t80)
REVERT: R  322 CYS cc_start: 0.8937 (m) cc_final: 0.8727 (m)
REVERT: R  335 MET cc_start: 0.9058 (mmt) cc_final: 0.8826 (mmp)
REVERT: R  382 LEU cc_start: 0.8938 (tp) cc_final: 0.8632 (tp)
REVERT: R  387 PHE cc_start: 0.9079 (t80) cc_final: 0.8848 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2206
  time to fit residues: 74.6687
Evaluate side-chains
  178 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 139 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    9.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 260 HIS
Q 373 ASN
Q 397 GLN
** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.057709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.044174 restraints weight = 74246.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.045609 restraints weight = 42388.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.046595 restraints weight = 28647.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12339  Z= 0.135
  Angle     :  0.613   8.332  16587  Z= 0.317
  Chirality :  0.040   0.137   1793
  Planarity :  0.004   0.044   2094
  Dihedral  :  5.231  22.634   1605
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  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:  0.17 (0.22), residues: 1440
  helix:  0.87 (0.16), residues: 1058
  sheet: -4.30 (0.74), residues: 17
  loop : -1.82 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 255 
 HIS   0.004   0.001   HIS E 304 
 PHE   0.024   0.001   PHE D  77 
 TYR   0.016   0.002   TYR Q 114 
 ARG   0.009   0.001   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  785)
  hydrogen bonds       : angle       4.26018 ( 2331)
  covalent geometry    : bond        0.00287 (12339)
  covalent geometry    : angle       0.61343 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.8840 (ttm) cc_final: 0.8612 (ttm)
REVERT: A  246 GLN cc_start: 0.7844 (pt0) cc_final: 0.7246 (pt0)
REVERT: A  263 MET cc_start: 0.9265 (mmm) cc_final: 0.9002 (mmm)
REVERT: A  267 THR cc_start: 0.8689 (m) cc_final: 0.8437 (m)
REVERT: A  322 ASP cc_start: 0.8953 (m-30) cc_final: 0.8581 (m-30)
REVERT: B   83 LEU cc_start: 0.8938 (mm) cc_final: 0.8684 (tp)
REVERT: B   91 LEU cc_start: 0.7849 (tt) cc_final: 0.7497 (mp)
REVERT: C  243 MET cc_start: 0.9305 (mtm) cc_final: 0.8815 (ttp)
REVERT: C  245 THR cc_start: 0.9672 (m) cc_final: 0.9329 (t)
REVERT: C  246 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: C  276 MET cc_start: 0.9032 (ttm) cc_final: 0.8710 (ttm)
REVERT: C  284 MET cc_start: 0.8585 (mtp) cc_final: 0.7791 (tmm)
REVERT: D   79 TYR cc_start: 0.8904 (t80) cc_final: 0.8566 (t80)
REVERT: D   97 ILE cc_start: 0.8213 (mt) cc_final: 0.7726 (tt)
REVERT: E  243 MET cc_start: 0.8372 (tpp) cc_final: 0.8000 (ttt)
REVERT: E  246 GLN cc_start: 0.9194 (tt0) cc_final: 0.8788 (tm-30)
REVERT: E  263 MET cc_start: 0.8287 (mmt) cc_final: 0.8072 (mmm)
REVERT: E  276 MET cc_start: 0.9282 (tpp) cc_final: 0.8802 (tpp)
REVERT: E  284 MET cc_start: 0.8093 (mtm) cc_final: 0.7893 (mtp)
REVERT: E  329 MET cc_start: 0.9052 (tpt) cc_final: 0.8732 (tpp)
REVERT: F   71 PHE cc_start: 0.7938 (m-80) cc_final: 0.7537 (m-80)
REVERT: F   83 LEU cc_start: 0.9109 (tt) cc_final: 0.8878 (mt)
REVERT: F   88 PHE cc_start: 0.8473 (t80) cc_final: 0.8153 (t80)
REVERT: F   92 LEU cc_start: 0.8855 (pp) cc_final: 0.8636 (pp)
REVERT: G  243 MET cc_start: 0.8659 (mtp) cc_final: 0.8291 (mtp)
REVERT: G  276 MET cc_start: 0.9079 (mtm) cc_final: 0.8650 (tmm)
REVERT: G  278 MET cc_start: 0.7962 (mmt) cc_final: 0.7727 (mmm)
REVERT: G  287 GLN cc_start: 0.8679 (tt0) cc_final: 0.8359 (tm-30)
REVERT: H   88 PHE cc_start: 0.8814 (t80) cc_final: 0.8582 (t80)
REVERT: H   92 LEU cc_start: 0.7659 (tp) cc_final: 0.7443 (pp)
REVERT: Q  130 TYR cc_start: 0.8266 (t80) cc_final: 0.7671 (t80)
REVERT: Q  176 PHE cc_start: 0.8138 (m-80) cc_final: 0.7416 (m-10)
REVERT: Q  208 ASP cc_start: 0.8874 (m-30) cc_final: 0.8629 (m-30)
REVERT: Q  228 LYS cc_start: 0.9227 (mttt) cc_final: 0.8957 (mttm)
REVERT: Q  229 MET cc_start: 0.8336 (mmm) cc_final: 0.8083 (mmm)
REVERT: Q  245 GLN cc_start: 0.9117 (mt0) cc_final: 0.8906 (mt0)
REVERT: Q  256 MET cc_start: 0.8289 (mmm) cc_final: 0.7946 (mmm)
REVERT: Q  330 MET cc_start: 0.8669 (tmm) cc_final: 0.8125 (tmm)
REVERT: Q  386 MET cc_start: 0.8630 (mtt) cc_final: 0.8272 (ttt)
REVERT: Q  393 LYS cc_start: 0.9159 (mttp) cc_final: 0.8878 (mtmm)
REVERT: Q  396 MET cc_start: 0.9008 (mtt) cc_final: 0.8743 (mtt)
REVERT: R   91 MET cc_start: 0.8376 (mtp) cc_final: 0.8042 (mmt)
REVERT: R  321 PHE cc_start: 0.9190 (t80) cc_final: 0.8871 (t80)
REVERT: R  322 CYS cc_start: 0.8942 (m) cc_final: 0.8727 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2308
  time to fit residues: 83.6736
Evaluate side-chains
  184 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 81 optimal weight:    9.9990
   chunk 59 optimal weight:    0.2980
   chunk 77 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 260 HIS
Q 295 ASN
** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 235 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 = 0.3227 r_free = 0.3227 target = 0.057855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.044329 restraints weight = 75111.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.045745 restraints weight = 43218.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.046645 restraints weight = 29470.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12339  Z= 0.135
  Angle     :  0.608   7.911  16587  Z= 0.313
  Chirality :  0.040   0.137   1793
  Planarity :  0.003   0.041   2094
  Dihedral  :  4.982  20.976   1605
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.08 %
    Favored  : 97.84 %
  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:  0.57 (0.22), residues: 1440
  helix:  1.17 (0.16), residues: 1058
  sheet: -3.88 (0.88), residues: 12
  loop : -1.77 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 256 
 HIS   0.004   0.001   HIS Q 411 
 PHE   0.026   0.002   PHE H  71 
 TYR   0.021   0.002   TYR E 268 
 ARG   0.008   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  785)
  hydrogen bonds       : angle       4.10113 ( 2331)
  covalent geometry    : bond        0.00286 (12339)
  covalent geometry    : angle       0.60811 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 1.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 GLN cc_start: 0.7893 (pt0) cc_final: 0.7207 (pt0)
REVERT: A  263 MET cc_start: 0.9224 (mmm) cc_final: 0.9010 (mmm)
REVERT: A  267 THR cc_start: 0.8710 (m) cc_final: 0.8482 (m)
REVERT: A  311 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8865 (mtm110)
REVERT: A  322 ASP cc_start: 0.8963 (m-30) cc_final: 0.8604 (m-30)
REVERT: B   80 VAL cc_start: 0.9406 (t) cc_final: 0.9183 (p)
REVERT: B   83 LEU cc_start: 0.8979 (mm) cc_final: 0.8610 (mp)
REVERT: B   91 LEU cc_start: 0.7784 (tt) cc_final: 0.7448 (mp)
REVERT: C  243 MET cc_start: 0.9278 (mtm) cc_final: 0.8802 (ttp)
REVERT: C  245 THR cc_start: 0.9665 (m) cc_final: 0.9368 (t)
REVERT: C  246 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: C  259 SER cc_start: 0.8123 (t) cc_final: 0.7878 (t)
REVERT: C  276 MET cc_start: 0.9112 (ttm) cc_final: 0.8776 (ttm)
REVERT: C  284 MET cc_start: 0.8686 (mtp) cc_final: 0.7849 (tmm)
REVERT: D   79 TYR cc_start: 0.8877 (t80) cc_final: 0.8675 (t80)
REVERT: D   97 ILE cc_start: 0.8211 (mt) cc_final: 0.7759 (tt)
REVERT: E  246 GLN cc_start: 0.9054 (tt0) cc_final: 0.8773 (tm-30)
REVERT: E  263 MET cc_start: 0.8228 (mmt) cc_final: 0.7670 (tpp)
REVERT: E  276 MET cc_start: 0.9200 (tpp) cc_final: 0.8645 (tpp)
REVERT: E  284 MET cc_start: 0.8208 (mtm) cc_final: 0.7936 (mtp)
REVERT: E  329 MET cc_start: 0.9061 (tpt) cc_final: 0.8712 (tpp)
REVERT: E  338 LEU cc_start: 0.8286 (tp) cc_final: 0.8076 (tp)
REVERT: F   71 PHE cc_start: 0.7961 (m-80) cc_final: 0.7535 (m-80)
REVERT: F   83 LEU cc_start: 0.9098 (tt) cc_final: 0.8891 (mt)
REVERT: F   88 PHE cc_start: 0.8559 (t80) cc_final: 0.8296 (t80)
REVERT: G  198 ASN cc_start: 0.7570 (m110) cc_final: 0.7025 (m-40)
REVERT: G  213 GLN cc_start: 0.9451 (mt0) cc_final: 0.9244 (mt0)
REVERT: G  243 MET cc_start: 0.8608 (mtp) cc_final: 0.8199 (mtp)
REVERT: G  276 MET cc_start: 0.9108 (mtm) cc_final: 0.8663 (tmm)
REVERT: G  287 GLN cc_start: 0.8704 (tt0) cc_final: 0.8365 (tm-30)
REVERT: Q  116 ASN cc_start: 0.9233 (m-40) cc_final: 0.9010 (m-40)
REVERT: Q  130 TYR cc_start: 0.8232 (t80) cc_final: 0.7792 (t80)
REVERT: Q  147 MET cc_start: 0.7648 (ptp) cc_final: 0.7156 (ptp)
REVERT: Q  176 PHE cc_start: 0.8201 (m-80) cc_final: 0.7501 (m-10)
REVERT: Q  208 ASP cc_start: 0.8835 (m-30) cc_final: 0.8608 (m-30)
REVERT: Q  229 MET cc_start: 0.8366 (mmm) cc_final: 0.8116 (mmm)
REVERT: Q  245 GLN cc_start: 0.9103 (mt0) cc_final: 0.8898 (mt0)
REVERT: Q  256 MET cc_start: 0.8222 (mmm) cc_final: 0.7851 (mmm)
REVERT: Q  330 MET cc_start: 0.8735 (tmm) cc_final: 0.8174 (tmm)
REVERT: Q  386 MET cc_start: 0.8657 (mtt) cc_final: 0.8290 (ttt)
REVERT: Q  445 LEU cc_start: 0.8426 (tp) cc_final: 0.7392 (tp)
REVERT: R   91 MET cc_start: 0.7969 (mtp) cc_final: 0.7495 (mmt)
REVERT: R  191 MET cc_start: 0.6367 (mmm) cc_final: 0.5309 (mmm)
REVERT: R  278 MET cc_start: 0.7263 (mmt) cc_final: 0.6989 (mmt)
REVERT: R  321 PHE cc_start: 0.9178 (t80) cc_final: 0.8879 (t80)
REVERT: R  322 CYS cc_start: 0.8945 (m) cc_final: 0.8716 (m)
REVERT: R  382 LEU cc_start: 0.8958 (tp) cc_final: 0.8642 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 240
  average time/residue: 0.2342
  time to fit residues: 81.7644
Evaluate side-chains
  188 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 115 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 127 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 36 optimal weight:   20.0000
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.057419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.043880 restraints weight = 75963.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.045309 restraints weight = 43179.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.046298 restraints weight = 29109.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12339  Z= 0.146
  Angle     :  0.616   7.828  16587  Z= 0.316
  Chirality :  0.040   0.137   1793
  Planarity :  0.004   0.041   2094
  Dihedral  :  4.904  21.079   1605
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  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:  0.73 (0.22), residues: 1440
  helix:  1.30 (0.16), residues: 1057
  sheet: -3.75 (0.88), residues: 12
  loop : -1.73 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 255 
 HIS   0.004   0.001   HIS E 304 
 PHE   0.028   0.002   PHE C 312 
 TYR   0.019   0.002   TYR E 268 
 ARG   0.009   0.000   ARG Q 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  785)
  hydrogen bonds       : angle       4.06095 ( 2331)
  covalent geometry    : bond        0.00312 (12339)
  covalent geometry    : angle       0.61595 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 GLN cc_start: 0.7850 (pt0) cc_final: 0.7285 (pt0)
REVERT: A  267 THR cc_start: 0.8704 (m) cc_final: 0.8444 (m)
REVERT: A  311 ARG cc_start: 0.9166 (mtt180) cc_final: 0.8857 (mtm110)
REVERT: B   83 LEU cc_start: 0.9040 (mm) cc_final: 0.8716 (mm)
REVERT: B   91 LEU cc_start: 0.7787 (tt) cc_final: 0.7432 (mp)
REVERT: C  243 MET cc_start: 0.9287 (mtm) cc_final: 0.8814 (ttp)
REVERT: C  245 THR cc_start: 0.9663 (m) cc_final: 0.9428 (p)
REVERT: C  246 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: C  259 SER cc_start: 0.8213 (t) cc_final: 0.8002 (t)
REVERT: C  284 MET cc_start: 0.8756 (mtp) cc_final: 0.7833 (tmm)
REVERT: D   97 ILE cc_start: 0.8244 (mt) cc_final: 0.7729 (tt)
REVERT: E  243 MET cc_start: 0.8596 (ttt) cc_final: 0.8135 (ttt)
REVERT: E  246 GLN cc_start: 0.9015 (tt0) cc_final: 0.8649 (tm-30)
REVERT: E  263 MET cc_start: 0.8239 (mmt) cc_final: 0.7737 (tpp)
REVERT: E  276 MET cc_start: 0.9142 (tpp) cc_final: 0.8714 (tpp)
REVERT: E  329 MET cc_start: 0.9072 (tpt) cc_final: 0.8762 (tpt)
REVERT: E  338 LEU cc_start: 0.8296 (tp) cc_final: 0.8093 (tp)
REVERT: F   67 LEU cc_start: 0.8397 (tt) cc_final: 0.8039 (mp)
REVERT: F   88 PHE cc_start: 0.8582 (t80) cc_final: 0.8325 (t80)
REVERT: G  243 MET cc_start: 0.8615 (mtp) cc_final: 0.8260 (mtp)
REVERT: G  276 MET cc_start: 0.9164 (mtm) cc_final: 0.8659 (tmm)
REVERT: G  287 GLN cc_start: 0.8688 (tt0) cc_final: 0.8328 (tm-30)
REVERT: H   67 LEU cc_start: 0.8956 (mt) cc_final: 0.8341 (pt)
REVERT: Q  118 ILE cc_start: 0.9462 (mt) cc_final: 0.8839 (mt)
REVERT: Q  130 TYR cc_start: 0.8422 (t80) cc_final: 0.8007 (t80)
REVERT: Q  147 MET cc_start: 0.8255 (ptp) cc_final: 0.7897 (ptp)
REVERT: Q  208 ASP cc_start: 0.8811 (m-30) cc_final: 0.8551 (m-30)
REVERT: Q  229 MET cc_start: 0.8357 (mmm) cc_final: 0.8131 (mmm)
REVERT: Q  256 MET cc_start: 0.8344 (mmm) cc_final: 0.7898 (mmm)
REVERT: Q  330 MET cc_start: 0.8824 (tmm) cc_final: 0.8308 (tmm)
REVERT: Q  386 MET cc_start: 0.8601 (mtt) cc_final: 0.8136 (ttt)
REVERT: Q  445 LEU cc_start: 0.8160 (tp) cc_final: 0.7816 (tp)
REVERT: R   91 MET cc_start: 0.7965 (mtp) cc_final: 0.7432 (mmt)
REVERT: R  191 MET cc_start: 0.6524 (mmm) cc_final: 0.6212 (mmm)
REVERT: R  278 MET cc_start: 0.7216 (mmt) cc_final: 0.6975 (mmt)
REVERT: R  321 PHE cc_start: 0.9173 (t80) cc_final: 0.8846 (t80)
REVERT: R  322 CYS cc_start: 0.8947 (m) cc_final: 0.8714 (m)
REVERT: R  382 LEU cc_start: 0.8960 (tp) cc_final: 0.8644 (tp)
REVERT: R  387 PHE cc_start: 0.9279 (t80) cc_final: 0.9000 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2717
  time to fit residues: 91.2928
Evaluate side-chains
  176 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 135 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 136 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 73 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    2.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 198 ASN
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 235 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 = 0.3221 r_free = 0.3221 target = 0.057633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.044259 restraints weight = 77056.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.045675 restraints weight = 44610.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.046632 restraints weight = 30284.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12339  Z= 0.147
  Angle     :  0.614   8.163  16587  Z= 0.317
  Chirality :  0.041   0.128   1793
  Planarity :  0.003   0.041   2094
  Dihedral  :  4.840  21.002   1605
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.46 %
    Favored  : 98.46 %
  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:  0.81 (0.22), residues: 1440
  helix:  1.37 (0.16), residues: 1057
  sheet: -3.57 (0.95), residues: 12
  loop : -1.72 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 255 
 HIS   0.004   0.001   HIS G 195 
 PHE   0.021   0.002   PHE H  88 
 TYR   0.021   0.002   TYR R 299 
 ARG   0.008   0.000   ARG C 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03719 (  785)
  hydrogen bonds       : angle       4.10561 ( 2331)
  covalent geometry    : bond        0.00314 (12339)
  covalent geometry    : angle       0.61421 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 1.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 LEU cc_start: 0.9471 (tp) cc_final: 0.9127 (tp)
REVERT: A  263 MET cc_start: 0.9252 (mmm) cc_final: 0.8920 (mmm)
REVERT: A  267 THR cc_start: 0.8603 (m) cc_final: 0.8356 (m)
REVERT: B   91 LEU cc_start: 0.7780 (tt) cc_final: 0.7426 (mp)
REVERT: C  243 MET cc_start: 0.9328 (mtm) cc_final: 0.8838 (ttp)
REVERT: C  245 THR cc_start: 0.9659 (m) cc_final: 0.9425 (p)
REVERT: C  246 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: C  284 MET cc_start: 0.8815 (mtp) cc_final: 0.7936 (tmm)
REVERT: D   97 ILE cc_start: 0.8266 (mt) cc_final: 0.7704 (tt)
REVERT: E  243 MET cc_start: 0.8429 (ttt) cc_final: 0.8021 (ttt)
REVERT: E  246 GLN cc_start: 0.9075 (tt0) cc_final: 0.8653 (tm-30)
REVERT: E  263 MET cc_start: 0.8261 (mmt) cc_final: 0.7653 (tpp)
REVERT: E  276 MET cc_start: 0.9182 (tpp) cc_final: 0.8779 (tpp)
REVERT: E  329 MET cc_start: 0.9065 (tpt) cc_final: 0.8661 (tpt)
REVERT: F   88 PHE cc_start: 0.8565 (t80) cc_final: 0.8309 (t80)
REVERT: G  243 MET cc_start: 0.8604 (mtp) cc_final: 0.8271 (mtp)
REVERT: G  276 MET cc_start: 0.9300 (mtm) cc_final: 0.8664 (tmm)
REVERT: G  287 GLN cc_start: 0.8794 (tt0) cc_final: 0.8427 (tm-30)
REVERT: H   57 LEU cc_start: 0.8710 (mt) cc_final: 0.8438 (mt)
REVERT: H   67 LEU cc_start: 0.8954 (mt) cc_final: 0.8346 (pt)
REVERT: Q  118 ILE cc_start: 0.9458 (mt) cc_final: 0.8978 (mt)
REVERT: Q  130 TYR cc_start: 0.8472 (t80) cc_final: 0.8021 (t80)
REVERT: Q  147 MET cc_start: 0.8353 (ptp) cc_final: 0.7944 (ptp)
REVERT: Q  208 ASP cc_start: 0.8802 (m-30) cc_final: 0.8544 (m-30)
REVERT: Q  256 MET cc_start: 0.8341 (mmm) cc_final: 0.7894 (mmm)
REVERT: Q  330 MET cc_start: 0.8804 (tmm) cc_final: 0.8257 (tmm)
REVERT: Q  386 MET cc_start: 0.8693 (mtt) cc_final: 0.8239 (ttt)
REVERT: Q  445 LEU cc_start: 0.8180 (tp) cc_final: 0.7832 (tp)
REVERT: R   91 MET cc_start: 0.7971 (mtp) cc_final: 0.7430 (mmt)
REVERT: R  191 MET cc_start: 0.6556 (mmm) cc_final: 0.6258 (mmm)
REVERT: R  266 MET cc_start: 0.9273 (mmp) cc_final: 0.9023 (mmp)
REVERT: R  278 MET cc_start: 0.7205 (mmt) cc_final: 0.6973 (mmt)
REVERT: R  299 TYR cc_start: 0.8642 (m-80) cc_final: 0.8010 (m-10)
REVERT: R  321 PHE cc_start: 0.9199 (t80) cc_final: 0.8848 (t80)
REVERT: R  322 CYS cc_start: 0.8955 (m) cc_final: 0.8730 (m)
REVERT: R  382 LEU cc_start: 0.8980 (tp) cc_final: 0.8684 (tp)
REVERT: R  387 PHE cc_start: 0.9370 (t80) cc_final: 0.9096 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 233
  average time/residue: 0.2516
  time to fit residues: 86.4444
Evaluate side-chains
  176 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 106 optimal weight:   30.0000
   chunk 47 optimal weight:    4.9990
   chunk 142 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 139 optimal weight:    0.0670
   chunk 100 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    3.5924

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 198 ASN
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 235 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 = 0.3203 r_free = 0.3203 target = 0.056974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.043566 restraints weight = 77863.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.044962 restraints weight = 44758.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.045898 restraints weight = 30420.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.4558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12339  Z= 0.176
  Angle     :  0.651   8.451  16587  Z= 0.336
  Chirality :  0.042   0.204   1793
  Planarity :  0.004   0.042   2094
  Dihedral  :  4.919  21.710   1605
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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:  0.82 (0.22), residues: 1440
  helix:  1.37 (0.16), residues: 1060
  sheet: -3.56 (0.95), residues: 12
  loop : -1.74 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 255 
 HIS   0.004   0.001   HIS G 195 
 PHE   0.021   0.002   PHE H  88 
 TYR   0.019   0.002   TYR E 268 
 ARG   0.006   0.001   ARG R 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03830 (  785)
  hydrogen bonds       : angle       4.18281 ( 2331)
  covalent geometry    : bond        0.00374 (12339)
  covalent geometry    : angle       0.65132 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.9160 (ttp) cc_final: 0.8782 (tmm)
REVERT: A  263 MET cc_start: 0.9177 (mmm) cc_final: 0.8884 (mmm)
REVERT: A  267 THR cc_start: 0.8630 (m) cc_final: 0.8362 (m)
REVERT: B   91 LEU cc_start: 0.7969 (tt) cc_final: 0.7649 (mp)
REVERT: C  243 MET cc_start: 0.9312 (mtm) cc_final: 0.8869 (ttp)
REVERT: C  245 THR cc_start: 0.9659 (m) cc_final: 0.9436 (p)
REVERT: C  246 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: C  259 SER cc_start: 0.8244 (t) cc_final: 0.8033 (t)
REVERT: C  284 MET cc_start: 0.8859 (mtp) cc_final: 0.7933 (tmm)
REVERT: D   97 ILE cc_start: 0.7938 (mt) cc_final: 0.7472 (tt)
REVERT: E  205 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8298 (pp20)
REVERT: E  243 MET cc_start: 0.8467 (ttt) cc_final: 0.8008 (ttt)
REVERT: E  246 GLN cc_start: 0.8992 (tt0) cc_final: 0.8653 (tm-30)
REVERT: E  263 MET cc_start: 0.8347 (mmt) cc_final: 0.7720 (tpp)
REVERT: E  276 MET cc_start: 0.9104 (tpp) cc_final: 0.8516 (tpp)
REVERT: E  329 MET cc_start: 0.9067 (tpt) cc_final: 0.8663 (tpt)
REVERT: F   67 LEU cc_start: 0.8777 (tt) cc_final: 0.8418 (pp)
REVERT: F   88 PHE cc_start: 0.8594 (t80) cc_final: 0.8347 (t80)
REVERT: G  243 MET cc_start: 0.8634 (mtp) cc_final: 0.8249 (mtp)
REVERT: G  276 MET cc_start: 0.9340 (mtm) cc_final: 0.8665 (tmm)
REVERT: G  287 GLN cc_start: 0.8688 (tt0) cc_final: 0.8323 (tm-30)
REVERT: G  335 ARG cc_start: 0.8617 (mmt180) cc_final: 0.8313 (ptt-90)
REVERT: H   57 LEU cc_start: 0.8725 (mt) cc_final: 0.8431 (mt)
REVERT: H   67 LEU cc_start: 0.8968 (mt) cc_final: 0.8361 (pt)
REVERT: Q  118 ILE cc_start: 0.9465 (mt) cc_final: 0.9016 (mt)
REVERT: Q  147 MET cc_start: 0.8417 (ptp) cc_final: 0.7975 (ptp)
REVERT: Q  208 ASP cc_start: 0.8884 (m-30) cc_final: 0.8661 (m-30)
REVERT: Q  245 GLN cc_start: 0.9097 (mt0) cc_final: 0.8881 (mt0)
REVERT: Q  256 MET cc_start: 0.8354 (mmm) cc_final: 0.7945 (mmm)
REVERT: Q  330 MET cc_start: 0.8735 (tmm) cc_final: 0.8172 (tmm)
REVERT: Q  386 MET cc_start: 0.8660 (mtt) cc_final: 0.8188 (ttt)
REVERT: Q  445 LEU cc_start: 0.8198 (tp) cc_final: 0.7840 (tp)
REVERT: R   91 MET cc_start: 0.8008 (mtp) cc_final: 0.7435 (mmt)
REVERT: R  191 MET cc_start: 0.6612 (mmm) cc_final: 0.5789 (mmm)
REVERT: R  266 MET cc_start: 0.9100 (mmp) cc_final: 0.8795 (mmp)
REVERT: R  299 TYR cc_start: 0.8645 (m-80) cc_final: 0.8108 (m-10)
REVERT: R  321 PHE cc_start: 0.9142 (t80) cc_final: 0.8780 (t80)
REVERT: R  322 CYS cc_start: 0.8997 (m) cc_final: 0.8747 (m)
REVERT: R  382 LEU cc_start: 0.9003 (tp) cc_final: 0.8718 (tp)
REVERT: R  387 PHE cc_start: 0.9360 (t80) cc_final: 0.9056 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.2408
  time to fit residues: 78.9834
Evaluate side-chains
  174 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 120 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 95 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 115 optimal weight:    6.9990
   chunk 106 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.056925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.043595 restraints weight = 76844.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.044997 restraints weight = 44325.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.045932 restraints weight = 30171.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.4610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12339  Z= 0.176
  Angle     :  0.659   9.180  16587  Z= 0.339
  Chirality :  0.042   0.200   1793
  Planarity :  0.004   0.043   2094
  Dihedral  :  4.917  21.569   1605
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  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:  0.79 (0.22), residues: 1440
  helix:  1.35 (0.16), residues: 1060
  sheet: -3.48 (0.99), residues: 12
  loop : -1.78 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 255 
 HIS   0.004   0.001   HIS G 195 
 PHE   0.028   0.002   PHE C 312 
 TYR   0.022   0.002   TYR E 268 
 ARG   0.006   0.001   ARG C 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03838 (  785)
  hydrogen bonds       : angle       4.21622 ( 2331)
  covalent geometry    : bond        0.00375 (12339)
  covalent geometry    : angle       0.65946 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.9121 (ttp) cc_final: 0.8842 (tmm)
REVERT: A  246 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8457 (pt0)
REVERT: A  263 MET cc_start: 0.9173 (mmm) cc_final: 0.8912 (mmm)
REVERT: A  267 THR cc_start: 0.8616 (m) cc_final: 0.8377 (m)
REVERT: B   59 LYS cc_start: 0.8955 (tptt) cc_final: 0.8277 (tppt)
REVERT: B   91 LEU cc_start: 0.7963 (tt) cc_final: 0.7631 (mp)
REVERT: C  243 MET cc_start: 0.9346 (mtm) cc_final: 0.8832 (ttp)
REVERT: C  245 THR cc_start: 0.9669 (m) cc_final: 0.9426 (p)
REVERT: C  246 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8166 (tm-30)
REVERT: C  284 MET cc_start: 0.8860 (mtp) cc_final: 0.7941 (tmm)
REVERT: D   97 ILE cc_start: 0.7966 (mt) cc_final: 0.7578 (tt)
REVERT: E  205 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8308 (pp20)
REVERT: E  243 MET cc_start: 0.8491 (ttt) cc_final: 0.7997 (ttt)
REVERT: E  246 GLN cc_start: 0.9104 (tt0) cc_final: 0.8653 (tm-30)
REVERT: E  263 MET cc_start: 0.8381 (mmt) cc_final: 0.7770 (tpp)
REVERT: E  276 MET cc_start: 0.9173 (tpp) cc_final: 0.8701 (tpp)
REVERT: E  329 MET cc_start: 0.9068 (tpt) cc_final: 0.8661 (tpt)
REVERT: F   71 PHE cc_start: 0.8155 (m-80) cc_final: 0.7898 (m-80)
REVERT: F   88 PHE cc_start: 0.8588 (t80) cc_final: 0.8345 (t80)
REVERT: G  243 MET cc_start: 0.8647 (mtp) cc_final: 0.8290 (mtp)
REVERT: G  276 MET cc_start: 0.9381 (mtm) cc_final: 0.8659 (tmm)
REVERT: G  287 GLN cc_start: 0.8722 (tt0) cc_final: 0.8342 (tm-30)
REVERT: H   57 LEU cc_start: 0.9150 (mt) cc_final: 0.8877 (mt)
REVERT: H   67 LEU cc_start: 0.8809 (mt) cc_final: 0.8268 (pt)
REVERT: Q  118 ILE cc_start: 0.9473 (mt) cc_final: 0.9005 (mt)
REVERT: Q  130 TYR cc_start: 0.8494 (t80) cc_final: 0.8029 (t80)
REVERT: Q  147 MET cc_start: 0.8429 (ptp) cc_final: 0.8005 (ptp)
REVERT: Q  208 ASP cc_start: 0.8892 (m-30) cc_final: 0.8674 (m-30)
REVERT: Q  256 MET cc_start: 0.8384 (mmm) cc_final: 0.8041 (mmm)
REVERT: Q  330 MET cc_start: 0.8734 (tmm) cc_final: 0.8175 (tmm)
REVERT: Q  386 MET cc_start: 0.8615 (mtt) cc_final: 0.8115 (ttt)
REVERT: Q  445 LEU cc_start: 0.8213 (tp) cc_final: 0.7845 (tp)
REVERT: R   91 MET cc_start: 0.8050 (mtp) cc_final: 0.7503 (mmt)
REVERT: R  191 MET cc_start: 0.6566 (mmm) cc_final: 0.5726 (mmm)
REVERT: R  266 MET cc_start: 0.9303 (mmp) cc_final: 0.9068 (mmp)
REVERT: R  299 TYR cc_start: 0.8650 (m-80) cc_final: 0.8033 (m-80)
REVERT: R  321 PHE cc_start: 0.9195 (t80) cc_final: 0.8806 (t80)
REVERT: R  322 CYS cc_start: 0.8973 (m) cc_final: 0.8735 (m)
REVERT: R  382 LEU cc_start: 0.9007 (tp) cc_final: 0.8704 (tp)
REVERT: R  387 PHE cc_start: 0.9377 (t80) cc_final: 0.9077 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.2167
  time to fit residues: 70.4529
Evaluate side-chains
  172 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 132 optimal weight:    8.9990
   chunk 91 optimal weight:   20.0000
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.057580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.044167 restraints weight = 75791.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.045584 restraints weight = 43305.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.046558 restraints weight = 29229.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.4743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12339  Z= 0.133
  Angle     :  0.649   8.777  16587  Z= 0.327
  Chirality :  0.041   0.188   1793
  Planarity :  0.004   0.044   2094
  Dihedral  :  4.827  20.346   1605
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  0.92 (0.22), residues: 1440
  helix:  1.45 (0.16), residues: 1060
  sheet: -3.45 (0.99), residues: 12
  loop : -1.75 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 256 
 HIS   0.004   0.001   HIS G 195 
 PHE   0.027   0.001   PHE H  88 
 TYR   0.020   0.002   TYR E 268 
 ARG   0.009   0.001   ARG G 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03697 (  785)
  hydrogen bonds       : angle       4.11156 ( 2331)
  covalent geometry    : bond        0.00287 (12339)
  covalent geometry    : angle       0.64855 (16587)

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

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

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2880 Ramachandran restraints generated.
    1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 1.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.9030 (ttp) cc_final: 0.8610 (tmm)
REVERT: A  246 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8371 (pt0)
REVERT: A  263 MET cc_start: 0.9215 (mmm) cc_final: 0.8904 (mmm)
REVERT: A  267 THR cc_start: 0.8697 (m) cc_final: 0.8457 (m)
REVERT: B   59 LYS cc_start: 0.8964 (tptt) cc_final: 0.8317 (tppt)
REVERT: B   91 LEU cc_start: 0.7941 (tt) cc_final: 0.7628 (mt)
REVERT: C  243 MET cc_start: 0.9252 (mtm) cc_final: 0.8706 (ttp)
REVERT: C  245 THR cc_start: 0.9666 (m) cc_final: 0.9399 (p)
REVERT: C  246 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: C  258 TYR cc_start: 0.6962 (t80) cc_final: 0.6708 (t80)
REVERT: C  284 MET cc_start: 0.8837 (mtp) cc_final: 0.7910 (tmm)
REVERT: D   97 ILE cc_start: 0.8067 (mt) cc_final: 0.7778 (tt)
REVERT: E  205 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8309 (pp20)
REVERT: E  243 MET cc_start: 0.8336 (ttt) cc_final: 0.8058 (ttt)
REVERT: E  246 GLN cc_start: 0.9019 (tt0) cc_final: 0.8710 (tm-30)
REVERT: E  263 MET cc_start: 0.8419 (mmt) cc_final: 0.7820 (tpp)
REVERT: E  329 MET cc_start: 0.9031 (tpt) cc_final: 0.8687 (tpt)
REVERT: F   71 PHE cc_start: 0.8112 (m-80) cc_final: 0.7787 (m-80)
REVERT: F   88 PHE cc_start: 0.8582 (t80) cc_final: 0.8354 (t80)
REVERT: G  213 GLN cc_start: 0.9449 (mt0) cc_final: 0.9247 (mt0)
REVERT: G  276 MET cc_start: 0.9322 (mtm) cc_final: 0.8652 (tmm)
REVERT: G  287 GLN cc_start: 0.8799 (tt0) cc_final: 0.8447 (tm-30)
REVERT: G  315 GLU cc_start: 0.9373 (pm20) cc_final: 0.9156 (pm20)
REVERT: H   57 LEU cc_start: 0.8576 (mt) cc_final: 0.8348 (mt)
REVERT: H   67 LEU cc_start: 0.8795 (mt) cc_final: 0.8274 (pt)
REVERT: Q  118 ILE cc_start: 0.9509 (mt) cc_final: 0.9126 (mt)
REVERT: Q  130 TYR cc_start: 0.8428 (t80) cc_final: 0.7966 (t80)
REVERT: Q  208 ASP cc_start: 0.8887 (m-30) cc_final: 0.8682 (m-30)
REVERT: Q  256 MET cc_start: 0.8302 (mmm) cc_final: 0.7948 (mmm)
REVERT: Q  330 MET cc_start: 0.8720 (tmm) cc_final: 0.8142 (tmm)
REVERT: Q  386 MET cc_start: 0.8599 (mtt) cc_final: 0.8120 (ttt)
REVERT: Q  445 LEU cc_start: 0.8172 (tp) cc_final: 0.7877 (tp)
REVERT: R   91 MET cc_start: 0.7999 (mtp) cc_final: 0.7429 (mmt)
REVERT: R  191 MET cc_start: 0.6368 (mmm) cc_final: 0.5508 (mmm)
REVERT: R  256 MET cc_start: 0.7883 (mtt) cc_final: 0.7672 (mtp)
REVERT: R  266 MET cc_start: 0.9279 (mmp) cc_final: 0.9051 (mmp)
REVERT: R  299 TYR cc_start: 0.8489 (m-80) cc_final: 0.7889 (m-80)
REVERT: R  321 PHE cc_start: 0.9196 (t80) cc_final: 0.8798 (t80)
REVERT: R  322 CYS cc_start: 0.8964 (m) cc_final: 0.8709 (m)
REVERT: R  382 LEU cc_start: 0.8994 (tp) cc_final: 0.8684 (tp)
REVERT: R  387 PHE cc_start: 0.9371 (t80) cc_final: 0.9070 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2830
  time to fit residues: 94.1002
Evaluate side-chains
  177 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 2.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0010
   chunk 115 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0170
   chunk 72 optimal weight:   10.0000
   chunk 130 optimal weight:   10.0000
   overall best weight:    1.6030

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 HIS
** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 235 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 = 0.3235 r_free = 0.3235 target = 0.058058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.044630 restraints weight = 74908.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.046061 restraints weight = 42996.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.047004 restraints weight = 29207.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12339  Z= 0.122
  Angle     :  0.631   8.573  16587  Z= 0.317
  Chirality :  0.041   0.179   1793
  Planarity :  0.003   0.041   2094
  Dihedral  :  4.732  19.687   1605
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 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:  1.02 (0.22), residues: 1440
  helix:  1.54 (0.16), residues: 1060
  sheet: -3.71 (0.86), residues: 12
  loop : -1.73 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 256 
 HIS   0.004   0.001   HIS G 195 
 PHE   0.027   0.001   PHE H  88 
 TYR   0.018   0.001   TYR E 268 
 ARG   0.006   0.000   ARG G 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 (  785)
  hydrogen bonds       : angle       4.06038 ( 2331)
  covalent geometry    : bond        0.00265 (12339)
  covalent geometry    : angle       0.63142 (16587)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4044.51 seconds
wall clock time: 73 minutes 53.08 seconds (4433.08 seconds total)