Starting phenix.real_space_refine
on Sat Aug 23 12:32:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xjx_22216/08_2025/6xjx_22216_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xjx_22216/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xjx_22216/08_2025/6xjx_22216_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xjx_22216/08_2025/6xjx_22216_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xjx_22216/08_2025/6xjx_22216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xjx_22216/08_2025/6xjx_22216.map"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.65, per 1000 atoms: 0.22
  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: 0.99
  Conformation dependent library (CDL) restraints added in 599.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.33
  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: 2.11

  Time building geometry restraints manager: 1.36 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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.890
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.820
-------------------------------------------------------------------------------
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 : 8.17
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.015   0.002   ARG C 252 
 TYR   0.031   0.004   TYR Q 114 
 PHE   0.035   0.004   PHE H  77 
 TRP   0.030   0.005   TRP A 255 
 HIS   0.014   0.003   HIS A 304 

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

*********************** 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  : 0.550 
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: 0.1280
  time to fit residues: 62.2734
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  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.0980
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0770
   overall best weight:    1.8342

-------------------------------------------------------------------------------
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 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 222 ASN
Q 260 HIS
Q 295 ASN
Q 352 HIS
** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 425 ASN
R 178 HIS
R 235 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.058444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.045132 restraints weight = 74097.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.046539 restraints weight = 42399.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.047485 restraints weight = 28627.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.048088 restraints weight = 21652.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.048525 restraints weight = 17883.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12339  Z= 0.145
  Angle     :  0.675   9.927  16587  Z= 0.349
  Chirality :  0.041   0.142   1793
  Planarity :  0.005   0.044   2094
  Dihedral  :  5.741  26.459   1605
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.20), residues: 1440
  helix: -0.13 (0.15), residues: 1053
  sheet: -4.31 (0.83), residues: 17
  loop : -2.17 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 252 
 TYR   0.023   0.002   TYR E 268 
 PHE   0.034   0.002   PHE Q 188 
 TRP   0.020   0.002   TRP C 255 
 HIS   0.005   0.001   HIS Q 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12339)
  covalent geometry    : angle       0.67549 (16587)
  hydrogen bonds       : bond        0.04344 (  785)
  hydrogen bonds       : angle       4.58938 ( 2331)

*********************** 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
  285 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 283
  time to evaluate  : 0.513 
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: A  243 MET cc_start: 0.9002 (ttm) cc_final: 0.8716 (ttm)
REVERT: A  267 THR cc_start: 0.8701 (m) cc_final: 0.8453 (m)
REVERT: A  278 MET cc_start: 0.8926 (mtt) cc_final: 0.8181 (mtm)
REVERT: A  322 ASP cc_start: 0.9093 (m-30) cc_final: 0.8746 (m-30)
REVERT: A  331 LEU cc_start: 0.8801 (mt) cc_final: 0.8547 (tp)
REVERT: A  335 ARG cc_start: 0.7780 (tmt170) cc_final: 0.7503 (tmt-80)
REVERT: B   80 VAL cc_start: 0.9386 (t) cc_final: 0.9166 (t)
REVERT: B   83 LEU cc_start: 0.9175 (mm) cc_final: 0.8660 (mp)
REVERT: B   91 LEU cc_start: 0.7902 (tt) cc_final: 0.7480 (mp)
REVERT: C  242 TYR cc_start: 0.9015 (t80) cc_final: 0.8781 (t80)
REVERT: C  243 MET cc_start: 0.9249 (mtm) cc_final: 0.8773 (mtm)
REVERT: C  246 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8530 (tm-30)
REVERT: C  276 MET cc_start: 0.9012 (ttm) cc_final: 0.8738 (ttm)
REVERT: C  284 MET cc_start: 0.8289 (mtp) cc_final: 0.7870 (tmm)
REVERT: D   79 TYR cc_start: 0.8801 (t80) cc_final: 0.8405 (t80)
REVERT: D   97 ILE cc_start: 0.8187 (mt) cc_final: 0.7574 (tt)
REVERT: E  201 ARG cc_start: 0.9414 (ttm110) cc_final: 0.8714 (ptp-110)
REVERT: E  202 GLU cc_start: 0.9384 (tt0) cc_final: 0.8727 (tm-30)
REVERT: E  205 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8312 (pp20)
REVERT: E  213 GLN cc_start: 0.9196 (tt0) cc_final: 0.8987 (tt0)
REVERT: E  243 MET cc_start: 0.8063 (tpt) cc_final: 0.7587 (ttm)
REVERT: E  246 GLN cc_start: 0.9136 (tt0) cc_final: 0.8626 (tm-30)
REVERT: E  262 ILE cc_start: 0.9596 (mt) cc_final: 0.9347 (mt)
REVERT: E  263 MET cc_start: 0.8142 (mmt) cc_final: 0.7818 (mmm)
REVERT: E  276 MET cc_start: 0.9199 (tpp) cc_final: 0.8859 (tpp)
REVERT: E  313 ASP cc_start: 0.9199 (m-30) cc_final: 0.8982 (p0)
REVERT: E  329 MET cc_start: 0.9023 (tpt) cc_final: 0.8704 (tpp)
REVERT: F   71 PHE cc_start: 0.8112 (m-80) cc_final: 0.7786 (m-80)
REVERT: F   83 LEU cc_start: 0.8873 (tt) cc_final: 0.8657 (mt)
REVERT: G  224 ILE cc_start: 0.9161 (mm) cc_final: 0.8721 (pt)
REVERT: G  276 MET cc_start: 0.8856 (mtm) cc_final: 0.8157 (mtp)
REVERT: G  315 GLU cc_start: 0.8994 (pm20) cc_final: 0.8791 (pm20)
REVERT: G  316 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8843 (mmmt)
REVERT: H   52 ARG cc_start: 0.8186 (mmt180) cc_final: 0.7972 (mtt180)
REVERT: H   67 LEU cc_start: 0.8458 (tt) cc_final: 0.8203 (pt)
REVERT: Q  125 ASP cc_start: 0.8750 (t0) cc_final: 0.8420 (t0)
REVERT: Q  204 ILE cc_start: 0.9346 (mt) cc_final: 0.9037 (tp)
REVERT: Q  208 ASP cc_start: 0.8782 (m-30) cc_final: 0.8488 (m-30)
REVERT: Q  213 THR cc_start: 0.9072 (m) cc_final: 0.8605 (p)
REVERT: Q  228 LYS cc_start: 0.9132 (mttt) cc_final: 0.8922 (mttm)
REVERT: Q  229 MET cc_start: 0.8299 (mmm) cc_final: 0.7654 (mmm)
REVERT: Q  245 GLN cc_start: 0.9122 (mt0) cc_final: 0.8886 (mt0)
REVERT: Q  256 MET cc_start: 0.8098 (mmm) cc_final: 0.7764 (mmm)
REVERT: Q  300 GLN cc_start: 0.9219 (tt0) cc_final: 0.8951 (tm-30)
REVERT: Q  330 MET cc_start: 0.8506 (tmm) cc_final: 0.8035 (tmm)
REVERT: Q  386 MET cc_start: 0.8514 (mtt) cc_final: 0.8171 (ttt)
REVERT: R   91 MET cc_start: 0.8376 (mtp) cc_final: 0.8076 (mmt)
REVERT: R  118 MET cc_start: 0.4264 (mmm) cc_final: 0.3687 (mtm)
REVERT: R  278 MET cc_start: 0.7302 (mmm) cc_final: 0.7013 (mmt)
REVERT: R  321 PHE cc_start: 0.9200 (t80) cc_final: 0.8844 (t80)
REVERT: R  322 CYS cc_start: 0.8984 (m) cc_final: 0.8754 (m)
REVERT: R  335 MET cc_start: 0.9055 (mmt) cc_final: 0.8830 (mmp)
REVERT: R  382 LEU cc_start: 0.8162 (tp) cc_final: 0.7910 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1025
  time to fit residues: 42.5757
Evaluate side-chains
  206 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 95 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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
** 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 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS
R 235 GLN
R 384 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.058894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.045461 restraints weight = 74100.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.046903 restraints weight = 42187.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.047805 restraints weight = 28468.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.048486 restraints weight = 21630.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.048879 restraints weight = 17849.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12339  Z= 0.120
  Angle     :  0.615   7.547  16587  Z= 0.312
  Chirality :  0.040   0.171   1793
  Planarity :  0.004   0.038   2094
  Dihedral  :  5.181  23.269   1605
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.85 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.21), residues: 1440
  helix:  0.55 (0.15), residues: 1063
  sheet: -3.91 (0.91), residues: 17
  loop : -2.03 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 201 
 TYR   0.023   0.001   TYR E 268 
 PHE   0.021   0.001   PHE D  77 
 TRP   0.010   0.001   TRP C 255 
 HIS   0.005   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12339)
  covalent geometry    : angle       0.61507 (16587)
  hydrogen bonds       : bond        0.03918 (  785)
  hydrogen bonds       : angle       4.24933 ( 2331)

*********************** 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
  273 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 272
  time to evaluate  : 0.427 
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: A  243 MET cc_start: 0.9001 (ttm) cc_final: 0.8710 (ttm)
REVERT: A  263 MET cc_start: 0.9136 (mmm) cc_final: 0.8836 (mmm)
REVERT: A  267 THR cc_start: 0.8770 (m) cc_final: 0.8549 (m)
REVERT: A  278 MET cc_start: 0.8811 (mtt) cc_final: 0.8086 (mtm)
REVERT: A  322 ASP cc_start: 0.8822 (m-30) cc_final: 0.8589 (m-30)
REVERT: A  331 LEU cc_start: 0.8810 (mt) cc_final: 0.8598 (tp)
REVERT: B   80 VAL cc_start: 0.9413 (t) cc_final: 0.9172 (t)
REVERT: B   83 LEU cc_start: 0.9062 (mm) cc_final: 0.8707 (mp)
REVERT: B   91 LEU cc_start: 0.7822 (tt) cc_final: 0.7503 (mp)
REVERT: C  243 MET cc_start: 0.9204 (mtm) cc_final: 0.8960 (ttp)
REVERT: C  246 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: C  259 SER cc_start: 0.8430 (t) cc_final: 0.7787 (m)
REVERT: C  276 MET cc_start: 0.8981 (ttm) cc_final: 0.8744 (ttm)
REVERT: C  284 MET cc_start: 0.8369 (mtp) cc_final: 0.7847 (tmm)
REVERT: C  290 VAL cc_start: 0.9053 (t) cc_final: 0.8663 (p)
REVERT: D   97 ILE cc_start: 0.7668 (mt) cc_final: 0.7229 (tt)
REVERT: E  213 GLN cc_start: 0.9107 (tt0) cc_final: 0.8848 (tt0)
REVERT: E  243 MET cc_start: 0.8385 (tpt) cc_final: 0.7721 (ttt)
REVERT: E  246 GLN cc_start: 0.9098 (tt0) cc_final: 0.8590 (tm-30)
REVERT: E  263 MET cc_start: 0.8034 (mmt) cc_final: 0.7747 (mmm)
REVERT: E  276 MET cc_start: 0.9200 (tpp) cc_final: 0.8720 (tpp)
REVERT: E  322 ASP cc_start: 0.9580 (t0) cc_final: 0.8848 (m-30)
REVERT: E  329 MET cc_start: 0.9142 (tpt) cc_final: 0.8753 (tpt)
REVERT: E  340 VAL cc_start: 0.7148 (m) cc_final: 0.6911 (t)
REVERT: F   71 PHE cc_start: 0.7963 (m-80) cc_final: 0.7526 (m-80)
REVERT: G  198 ASN cc_start: 0.7491 (m110) cc_final: 0.6910 (m110)
REVERT: G  213 GLN cc_start: 0.9401 (mt0) cc_final: 0.9160 (mt0)
REVERT: G  246 GLN cc_start: 0.8792 (tt0) cc_final: 0.8482 (tt0)
REVERT: G  270 ILE cc_start: 0.8895 (mt) cc_final: 0.8688 (tt)
REVERT: G  276 MET cc_start: 0.9002 (mtm) cc_final: 0.8626 (tmm)
REVERT: G  278 MET cc_start: 0.8721 (mmm) cc_final: 0.8409 (mmt)
REVERT: G  316 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8871 (mmmt)
REVERT: H   52 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7983 (mtt180)
REVERT: H   57 LEU cc_start: 0.8578 (mt) cc_final: 0.8286 (mt)
REVERT: H   67 LEU cc_start: 0.8417 (tt) cc_final: 0.8185 (pt)
REVERT: Q  125 ASP cc_start: 0.8707 (t0) cc_final: 0.8348 (t0)
REVERT: Q  130 TYR cc_start: 0.8262 (t80) cc_final: 0.7869 (t80)
REVERT: Q  208 ASP cc_start: 0.8941 (m-30) cc_final: 0.8677 (m-30)
REVERT: Q  228 LYS cc_start: 0.9216 (mttt) cc_final: 0.8910 (mttm)
REVERT: Q  229 MET cc_start: 0.8259 (mmm) cc_final: 0.8018 (mmp)
REVERT: Q  245 GLN cc_start: 0.9120 (mt0) cc_final: 0.8919 (mt0)
REVERT: Q  256 MET cc_start: 0.8238 (mmm) cc_final: 0.7868 (mmm)
REVERT: Q  330 MET cc_start: 0.8674 (tmm) cc_final: 0.8043 (tmm)
REVERT: Q  386 MET cc_start: 0.8523 (mtt) cc_final: 0.8223 (ttt)
REVERT: R   91 MET cc_start: 0.8195 (mtp) cc_final: 0.7959 (mmt)
REVERT: R  118 MET cc_start: 0.4240 (mmm) cc_final: 0.3855 (mtm)
REVERT: R  278 MET cc_start: 0.7457 (mmm) cc_final: 0.6274 (tpp)
REVERT: R  299 TYR cc_start: 0.8382 (m-80) cc_final: 0.7957 (m-10)
REVERT: R  321 PHE cc_start: 0.9177 (t80) cc_final: 0.8869 (t80)
REVERT: R  322 CYS cc_start: 0.8989 (m) cc_final: 0.8714 (m)
REVERT: R  379 ASP cc_start: 0.7231 (m-30) cc_final: 0.6740 (p0)
REVERT: R  382 LEU cc_start: 0.8860 (tp) cc_final: 0.8554 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 273
  average time/residue: 0.1012
  time to fit residues: 40.3889
Evaluate side-chains
  199 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 125 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 120 optimal weight:   10.0000
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 397 GLN
R 235 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.057236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.043700 restraints weight = 74956.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.045163 restraints weight = 42494.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.046093 restraints weight = 28508.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.046762 restraints weight = 21659.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.047192 restraints weight = 17714.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12339  Z= 0.172
  Angle     :  0.626   7.786  16587  Z= 0.325
  Chirality :  0.040   0.139   1793
  Planarity :  0.004   0.039   2094
  Dihedral  :  5.053  23.146   1605
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.22), residues: 1440
  helix:  0.98 (0.16), residues: 1057
  sheet: -4.16 (0.72), residues: 17
  loop : -1.70 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 201 
 TYR   0.015   0.002   TYR Q 114 
 PHE   0.022   0.002   PHE D  77 
 TRP   0.011   0.001   TRP A 255 
 HIS   0.004   0.001   HIS Q 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12339)
  covalent geometry    : angle       0.62592 (16587)
  hydrogen bonds       : bond        0.03913 (  785)
  hydrogen bonds       : angle       4.23187 ( 2331)

*********************** 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
  250 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.9019 (ttm) cc_final: 0.8745 (ttm)
REVERT: A  263 MET cc_start: 0.9183 (mmm) cc_final: 0.8982 (mmm)
REVERT: A  278 MET cc_start: 0.8864 (mtt) cc_final: 0.8535 (mmt)
REVERT: A  322 ASP cc_start: 0.8923 (m-30) cc_final: 0.8632 (m-30)
REVERT: A  331 LEU cc_start: 0.8863 (mt) cc_final: 0.8628 (tp)
REVERT: A  335 ARG cc_start: 0.7852 (tmt170) cc_final: 0.7484 (tpt90)
REVERT: B   83 LEU cc_start: 0.8954 (mm) cc_final: 0.8674 (tp)
REVERT: B   91 LEU cc_start: 0.7878 (tt) cc_final: 0.7543 (mp)
REVERT: C  243 MET cc_start: 0.9303 (mtm) cc_final: 0.8924 (ttp)
REVERT: C  246 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: C  259 SER cc_start: 0.8338 (t) cc_final: 0.7925 (t)
REVERT: C  276 MET cc_start: 0.9044 (ttm) cc_final: 0.8804 (ttm)
REVERT: C  284 MET cc_start: 0.8526 (mtp) cc_final: 0.7717 (tmm)
REVERT: D   97 ILE cc_start: 0.8169 (mt) cc_final: 0.7706 (tt)
REVERT: E  213 GLN cc_start: 0.9261 (tt0) cc_final: 0.9052 (tt0)
REVERT: E  243 MET cc_start: 0.8224 (tpt) cc_final: 0.7716 (tpp)
REVERT: E  246 GLN cc_start: 0.9089 (tt0) cc_final: 0.8616 (tm-30)
REVERT: E  263 MET cc_start: 0.8150 (mmt) cc_final: 0.7839 (mmm)
REVERT: E  276 MET cc_start: 0.9298 (tpp) cc_final: 0.8761 (tpp)
REVERT: E  311 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8308 (mtm110)
REVERT: E  329 MET cc_start: 0.9070 (tpt) cc_final: 0.8744 (tpp)
REVERT: F   71 PHE cc_start: 0.7971 (m-80) cc_final: 0.7537 (m-80)
REVERT: F   88 PHE cc_start: 0.8601 (t80) cc_final: 0.8313 (t80)
REVERT: F   92 LEU cc_start: 0.8939 (pp) cc_final: 0.8721 (pp)
REVERT: G  198 ASN cc_start: 0.7434 (m110) cc_final: 0.6900 (m110)
REVERT: G  243 MET cc_start: 0.8620 (ttt) cc_final: 0.6536 (ttt)
REVERT: G  276 MET cc_start: 0.9102 (mtm) cc_final: 0.8683 (tmm)
REVERT: H   52 ARG cc_start: 0.8365 (mmt180) cc_final: 0.8050 (mtt180)
REVERT: H   67 LEU cc_start: 0.8413 (tt) cc_final: 0.8147 (pt)
REVERT: H   92 LEU cc_start: 0.7516 (tp) cc_final: 0.7286 (pp)
REVERT: Q  118 ILE cc_start: 0.9446 (mt) cc_final: 0.8881 (mt)
REVERT: Q  130 TYR cc_start: 0.8268 (t80) cc_final: 0.7622 (t80)
REVERT: Q  147 MET cc_start: 0.8217 (ptp) cc_final: 0.7600 (ptp)
REVERT: Q  208 ASP cc_start: 0.8887 (m-30) cc_final: 0.8612 (m-30)
REVERT: Q  228 LYS cc_start: 0.9261 (mttt) cc_final: 0.8943 (mttm)
REVERT: Q  229 MET cc_start: 0.8411 (mmm) cc_final: 0.8128 (mmp)
REVERT: Q  256 MET cc_start: 0.8250 (mmm) cc_final: 0.7868 (mmm)
REVERT: Q  330 MET cc_start: 0.8695 (tmm) cc_final: 0.8219 (tmm)
REVERT: Q  386 MET cc_start: 0.8621 (mtt) cc_final: 0.8288 (ttt)
REVERT: Q  431 LYS cc_start: 0.8667 (mptt) cc_final: 0.8434 (pttm)
REVERT: R   91 MET cc_start: 0.7989 (mtp) cc_final: 0.7552 (mmt)
REVERT: R  118 MET cc_start: 0.4514 (mmm) cc_final: 0.4075 (mtm)
REVERT: R  191 MET cc_start: 0.6461 (mmm) cc_final: 0.6156 (mmm)
REVERT: R  278 MET cc_start: 0.7502 (mmm) cc_final: 0.7211 (mmt)
REVERT: R  299 TYR cc_start: 0.8441 (m-80) cc_final: 0.8006 (m-10)
REVERT: R  321 PHE cc_start: 0.9361 (t80) cc_final: 0.9134 (t80)
REVERT: R  322 CYS cc_start: 0.8992 (m) cc_final: 0.8757 (m)
REVERT: R  365 ASN cc_start: 0.8559 (p0) cc_final: 0.8242 (p0)
REVERT: R  382 LEU cc_start: 0.8939 (tp) cc_final: 0.8594 (tp)
REVERT: R  387 PHE cc_start: 0.9037 (t80) cc_final: 0.8816 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.0930
  time to fit residues: 33.9443
Evaluate side-chains
  185 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 130 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 138 optimal weight:    9.9990
   chunk 104 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 128 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   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**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 339 GLN
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 235 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.056982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.043536 restraints weight = 75798.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.044912 restraints weight = 43541.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.045873 restraints weight = 29630.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.046492 restraints weight = 22548.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.046838 restraints weight = 18666.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12339  Z= 0.175
  Angle     :  0.629   7.873  16587  Z= 0.326
  Chirality :  0.041   0.150   1793
  Planarity :  0.004   0.042   2094
  Dihedral  :  4.960  22.224   1605
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.22), residues: 1440
  helix:  1.19 (0.16), residues: 1058
  sheet: -4.22 (0.70), residues: 17
  loop : -1.66 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Q 261 
 TYR   0.014   0.002   TYR D  79 
 PHE   0.028   0.002   PHE C 312 
 TRP   0.012   0.002   TRP C 255 
 HIS   0.005   0.001   HIS Q 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (12339)
  covalent geometry    : angle       0.62926 (16587)
  hydrogen bonds       : bond        0.03874 (  785)
  hydrogen bonds       : angle       4.21242 ( 2331)

*********************** 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
  233 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.384 
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: 0.9018 (ttm) cc_final: 0.8730 (ttm)
REVERT: A  331 LEU cc_start: 0.8885 (mt) cc_final: 0.8666 (tp)
REVERT: B   59 LYS cc_start: 0.9054 (tptm) cc_final: 0.8807 (tptt)
REVERT: B   83 LEU cc_start: 0.9032 (mm) cc_final: 0.8710 (mm)
REVERT: B   91 LEU cc_start: 0.7809 (tt) cc_final: 0.7466 (mp)
REVERT: C  243 MET cc_start: 0.9287 (mtm) cc_final: 0.8968 (ttp)
REVERT: C  246 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8395 (tm-30)
REVERT: C  259 SER cc_start: 0.8311 (t) cc_final: 0.8025 (t)
REVERT: C  276 MET cc_start: 0.9014 (ttm) cc_final: 0.8725 (ttm)
REVERT: C  284 MET cc_start: 0.8628 (mtp) cc_final: 0.7726 (tmm)
REVERT: D   97 ILE cc_start: 0.8118 (mt) cc_final: 0.7659 (tt)
REVERT: E  243 MET cc_start: 0.8276 (tpt) cc_final: 0.7800 (tpp)
REVERT: E  246 GLN cc_start: 0.9074 (tt0) cc_final: 0.8648 (tm-30)
REVERT: E  263 MET cc_start: 0.8273 (mmt) cc_final: 0.7994 (mmm)
REVERT: E  311 ARG cc_start: 0.8737 (mtm180) cc_final: 0.7521 (ttp80)
REVERT: E  329 MET cc_start: 0.9099 (tpt) cc_final: 0.8761 (tpp)
REVERT: F   71 PHE cc_start: 0.7942 (m-80) cc_final: 0.7526 (m-80)
REVERT: F   88 PHE cc_start: 0.8600 (t80) cc_final: 0.8319 (t80)
REVERT: G  276 MET cc_start: 0.9195 (mtm) cc_final: 0.8694 (tmm)
REVERT: G  287 GLN cc_start: 0.8523 (tt0) cc_final: 0.8109 (tm-30)
REVERT: H   67 LEU cc_start: 0.8338 (tt) cc_final: 0.8074 (pt)
REVERT: Q  112 MET cc_start: 0.9100 (ttt) cc_final: 0.8895 (mmm)
REVERT: Q  118 ILE cc_start: 0.9426 (mt) cc_final: 0.8930 (mt)
REVERT: Q  125 ASP cc_start: 0.8732 (t0) cc_final: 0.8485 (t0)
REVERT: Q  130 TYR cc_start: 0.8203 (t80) cc_final: 0.7751 (t80)
REVERT: Q  147 MET cc_start: 0.8463 (ptp) cc_final: 0.8019 (ptp)
REVERT: Q  208 ASP cc_start: 0.8872 (m-30) cc_final: 0.8639 (m-30)
REVERT: Q  229 MET cc_start: 0.8371 (mmm) cc_final: 0.8091 (mmm)
REVERT: Q  245 GLN cc_start: 0.9107 (mt0) cc_final: 0.8897 (mt0)
REVERT: Q  256 MET cc_start: 0.8364 (mmm) cc_final: 0.7932 (mmm)
REVERT: Q  330 MET cc_start: 0.8727 (tmm) cc_final: 0.8263 (tmm)
REVERT: Q  386 MET cc_start: 0.8643 (mtt) cc_final: 0.8301 (ttt)
REVERT: Q  445 LEU cc_start: 0.8524 (tp) cc_final: 0.7618 (tp)
REVERT: R   91 MET cc_start: 0.8005 (mtp) cc_final: 0.7486 (mmt)
REVERT: R  191 MET cc_start: 0.6533 (mmm) cc_final: 0.6229 (mmm)
REVERT: R  299 TYR cc_start: 0.8270 (m-80) cc_final: 0.7801 (m-10)
REVERT: R  321 PHE cc_start: 0.9308 (t80) cc_final: 0.9006 (t80)
REVERT: R  322 CYS cc_start: 0.9013 (m) cc_final: 0.8768 (m)
REVERT: R  382 LEU cc_start: 0.8967 (tp) cc_final: 0.8728 (tp)
REVERT: R  387 PHE cc_start: 0.9049 (t80) cc_final: 0.8838 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.0894
  time to fit residues: 31.2884
Evaluate side-chains
  175 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 106 optimal weight:   30.0000
   chunk 134 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 117 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 198 ASN
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 235 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.057485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.044067 restraints weight = 76010.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.045458 restraints weight = 43959.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.046410 restraints weight = 29957.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.047047 restraints weight = 22908.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.047403 restraints weight = 18916.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12339  Z= 0.155
  Angle     :  0.624   7.500  16587  Z= 0.321
  Chirality :  0.041   0.152   1793
  Planarity :  0.004   0.048   2094
  Dihedral  :  4.852  21.312   1605
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.24 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.22), residues: 1440
  helix:  1.28 (0.16), residues: 1057
  sheet: -4.29 (0.70), residues: 17
  loop : -1.57 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG Q 261 
 TYR   0.022   0.002   TYR A 289 
 PHE   0.020   0.001   PHE H  88 
 TRP   0.012   0.001   TRP C 255 
 HIS   0.004   0.001   HIS E 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (12339)
  covalent geometry    : angle       0.62356 (16587)
  hydrogen bonds       : bond        0.03781 (  785)
  hydrogen bonds       : angle       4.13675 ( 2331)

*********************** 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
  229 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 0.491 
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  243 MET cc_start: 0.8991 (ttm) cc_final: 0.8686 (ttm)
REVERT: A  263 MET cc_start: 0.9186 (mmm) cc_final: 0.8936 (mmm)
REVERT: A  267 THR cc_start: 0.8651 (m) cc_final: 0.8446 (m)
REVERT: A  335 ARG cc_start: 0.7649 (tmt170) cc_final: 0.7363 (tmt-80)
REVERT: B   83 LEU cc_start: 0.9029 (mm) cc_final: 0.8725 (mm)
REVERT: B   91 LEU cc_start: 0.7793 (tt) cc_final: 0.7447 (mp)
REVERT: C  243 MET cc_start: 0.9261 (mtm) cc_final: 0.8974 (ttp)
REVERT: C  246 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: C  276 MET cc_start: 0.9028 (ttm) cc_final: 0.8720 (ttm)
REVERT: C  278 MET cc_start: 0.8193 (mmp) cc_final: 0.7677 (mmp)
REVERT: C  284 MET cc_start: 0.8688 (mtp) cc_final: 0.7804 (tmm)
REVERT: D   97 ILE cc_start: 0.8210 (mt) cc_final: 0.7708 (tt)
REVERT: E  243 MET cc_start: 0.8127 (tpt) cc_final: 0.7598 (tpp)
REVERT: E  246 GLN cc_start: 0.9077 (tt0) cc_final: 0.8758 (tm-30)
REVERT: E  263 MET cc_start: 0.8258 (mmt) cc_final: 0.8013 (mmm)
REVERT: E  276 MET cc_start: 0.9108 (tpp) cc_final: 0.8417 (tpp)
REVERT: E  329 MET cc_start: 0.9044 (tpt) cc_final: 0.8700 (tpt)
REVERT: F   67 LEU cc_start: 0.8633 (tt) cc_final: 0.8053 (mp)
REVERT: F   88 PHE cc_start: 0.8599 (t80) cc_final: 0.8336 (t80)
REVERT: G  243 MET cc_start: 0.8628 (ttt) cc_final: 0.7435 (ttt)
REVERT: G  276 MET cc_start: 0.9187 (mtm) cc_final: 0.8681 (tmm)
REVERT: G  287 GLN cc_start: 0.8513 (tt0) cc_final: 0.8140 (tm-30)
REVERT: H   67 LEU cc_start: 0.8322 (tt) cc_final: 0.8051 (pt)
REVERT: Q  118 ILE cc_start: 0.9459 (mt) cc_final: 0.8984 (mt)
REVERT: Q  125 ASP cc_start: 0.8667 (t0) cc_final: 0.8405 (t0)
REVERT: Q  130 TYR cc_start: 0.8252 (t80) cc_final: 0.7820 (t80)
REVERT: Q  147 MET cc_start: 0.8508 (ptp) cc_final: 0.8059 (ptp)
REVERT: Q  208 ASP cc_start: 0.8926 (m-30) cc_final: 0.8657 (m-30)
REVERT: Q  256 MET cc_start: 0.8300 (mmm) cc_final: 0.7849 (mmm)
REVERT: Q  330 MET cc_start: 0.8762 (tmm) cc_final: 0.8285 (tmm)
REVERT: Q  386 MET cc_start: 0.8593 (mtt) cc_final: 0.8106 (ttt)
REVERT: Q  445 LEU cc_start: 0.8266 (tp) cc_final: 0.7933 (tp)
REVERT: R   91 MET cc_start: 0.8173 (mtp) cc_final: 0.7460 (mmt)
REVERT: R  191 MET cc_start: 0.6554 (mmm) cc_final: 0.5741 (mmm)
REVERT: R  278 MET cc_start: 0.7082 (mmt) cc_final: 0.6566 (mmt)
REVERT: R  299 TYR cc_start: 0.8298 (m-80) cc_final: 0.7653 (m-10)
REVERT: R  321 PHE cc_start: 0.9320 (t80) cc_final: 0.8985 (t80)
REVERT: R  322 CYS cc_start: 0.9013 (m) cc_final: 0.8760 (m)
REVERT: R  382 LEU cc_start: 0.8980 (tp) cc_final: 0.8740 (tp)
REVERT: R  387 PHE cc_start: 0.9052 (t80) cc_final: 0.8781 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.0954
  time to fit residues: 32.3807
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  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 135 optimal weight:    5.9990
   chunk 133 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 118 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 114 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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
** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 295 ASN
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 235 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.058475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.044978 restraints weight = 74394.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.046407 restraints weight = 42948.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.047376 restraints weight = 29143.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.048019 restraints weight = 22109.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.048408 restraints weight = 18239.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4519

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= 0.120
  Angle     :  0.613   7.765  16587  Z= 0.312
  Chirality :  0.040   0.140   1793
  Planarity :  0.004   0.076   2094
  Dihedral  :  4.753  20.751   1605
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.22), residues: 1440
  helix:  1.37 (0.16), residues: 1061
  sheet: -4.10 (0.74), residues: 17
  loop : -1.62 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 252 
 TYR   0.025   0.001   TYR A 289 
 PHE   0.022   0.001   PHE H  88 
 TRP   0.009   0.001   TRP C 255 
 HIS   0.003   0.001   HIS G 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12339)
  covalent geometry    : angle       0.61276 (16587)
  hydrogen bonds       : bond        0.03676 (  785)
  hydrogen bonds       : angle       4.04209 ( 2331)

*********************** 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
  234 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.505 
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  214 LEU cc_start: 0.9328 (tp) cc_final: 0.9000 (tp)
REVERT: A  218 GLU cc_start: 0.9066 (pt0) cc_final: 0.8791 (pm20)
REVERT: A  243 MET cc_start: 0.8969 (ttm) cc_final: 0.8662 (ttm)
REVERT: A  263 MET cc_start: 0.9109 (mmm) cc_final: 0.8831 (mmm)
REVERT: A  267 THR cc_start: 0.8618 (m) cc_final: 0.8382 (m)
REVERT: A  335 ARG cc_start: 0.7825 (tmt170) cc_final: 0.7568 (tmt-80)
REVERT: B   80 VAL cc_start: 0.9199 (m) cc_final: 0.8992 (m)
REVERT: B   83 LEU cc_start: 0.8978 (mm) cc_final: 0.8712 (mp)
REVERT: B   91 LEU cc_start: 0.7917 (tt) cc_final: 0.7632 (mp)
REVERT: C  243 MET cc_start: 0.9258 (mtm) cc_final: 0.8928 (ttp)
REVERT: C  246 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8394 (tm-30)
REVERT: C  276 MET cc_start: 0.9010 (ttm) cc_final: 0.8706 (ttm)
REVERT: C  284 MET cc_start: 0.8670 (mtp) cc_final: 0.7876 (tmm)
REVERT: D   97 ILE cc_start: 0.8223 (mt) cc_final: 0.7722 (tt)
REVERT: E  243 MET cc_start: 0.8039 (tpt) cc_final: 0.7454 (tpp)
REVERT: E  246 GLN cc_start: 0.9126 (tt0) cc_final: 0.8797 (tm-30)
REVERT: E  263 MET cc_start: 0.8125 (mmt) cc_final: 0.7679 (tpp)
REVERT: E  276 MET cc_start: 0.9152 (tpp) cc_final: 0.8569 (tpp)
REVERT: E  329 MET cc_start: 0.9005 (tpt) cc_final: 0.8754 (tpt)
REVERT: F   88 PHE cc_start: 0.8553 (t80) cc_final: 0.8275 (t80)
REVERT: G  243 MET cc_start: 0.8610 (ttt) cc_final: 0.7317 (ttt)
REVERT: G  276 MET cc_start: 0.9226 (mtm) cc_final: 0.8663 (tmm)
REVERT: G  287 GLN cc_start: 0.8808 (tt0) cc_final: 0.8443 (tm-30)
REVERT: H   57 LEU cc_start: 0.8764 (mt) cc_final: 0.8485 (mt)
REVERT: Q  125 ASP cc_start: 0.8591 (t0) cc_final: 0.8337 (t0)
REVERT: Q  130 TYR cc_start: 0.8329 (t80) cc_final: 0.7945 (t80)
REVERT: Q  208 ASP cc_start: 0.8875 (m-30) cc_final: 0.8639 (m-30)
REVERT: Q  229 MET cc_start: 0.8539 (mmp) cc_final: 0.8080 (mmp)
REVERT: Q  256 MET cc_start: 0.8146 (mmm) cc_final: 0.7730 (mmm)
REVERT: Q  330 MET cc_start: 0.8651 (tmm) cc_final: 0.8187 (tmm)
REVERT: Q  386 MET cc_start: 0.8588 (mtt) cc_final: 0.8129 (ttt)
REVERT: Q  393 LYS cc_start: 0.9127 (mttp) cc_final: 0.8888 (mtmm)
REVERT: Q  445 LEU cc_start: 0.8199 (tp) cc_final: 0.7922 (tp)
REVERT: R   91 MET cc_start: 0.8142 (mtp) cc_final: 0.7415 (mmm)
REVERT: R  278 MET cc_start: 0.7108 (mmt) cc_final: 0.6678 (mmt)
REVERT: R  299 TYR cc_start: 0.8356 (m-80) cc_final: 0.7851 (m-10)
REVERT: R  321 PHE cc_start: 0.9256 (t80) cc_final: 0.8865 (t80)
REVERT: R  322 CYS cc_start: 0.9003 (m) cc_final: 0.8738 (m)
REVERT: R  382 LEU cc_start: 0.8959 (tp) cc_final: 0.8686 (tp)
REVERT: R  387 PHE cc_start: 0.9046 (t80) cc_final: 0.8809 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.0927
  time to fit residues: 32.4237
Evaluate side-chains
  181 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 136 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 92 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0770
   overall best weight:    1.1744

-------------------------------------------------------------------------------
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**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 304 HIS
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 235 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.058798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.045467 restraints weight = 74099.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.046888 restraints weight = 42906.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.047867 restraints weight = 29267.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.048503 restraints weight = 22190.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.048883 restraints weight = 18322.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12339  Z= 0.121
  Angle     :  0.630   8.143  16587  Z= 0.320
  Chirality :  0.041   0.193   1793
  Planarity :  0.005   0.158   2094
  Dihedral  :  4.711  20.663   1605
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.22), residues: 1440
  helix:  1.45 (0.16), residues: 1062
  sheet: -4.23 (0.66), residues: 17
  loop : -1.62 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 394 
 TYR   0.023   0.001   TYR A 289 
 PHE   0.024   0.001   PHE H  88 
 TRP   0.010   0.001   TRP C 255 
 HIS   0.004   0.001   HIS E 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12339)
  covalent geometry    : angle       0.63026 (16587)
  hydrogen bonds       : bond        0.03697 (  785)
  hydrogen bonds       : angle       3.99691 ( 2331)

*********************** 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
  229 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.418 
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  214 LEU cc_start: 0.9320 (tp) cc_final: 0.8979 (tp)
REVERT: A  218 GLU cc_start: 0.9097 (pt0) cc_final: 0.8622 (pm20)
REVERT: A  243 MET cc_start: 0.8954 (ttm) cc_final: 0.8696 (ttm)
REVERT: A  263 MET cc_start: 0.9081 (mmm) cc_final: 0.8823 (mmm)
REVERT: A  267 THR cc_start: 0.8635 (m) cc_final: 0.8375 (m)
REVERT: B   80 VAL cc_start: 0.9297 (m) cc_final: 0.9082 (m)
REVERT: B   83 LEU cc_start: 0.8948 (mm) cc_final: 0.8640 (mp)
REVERT: B   91 LEU cc_start: 0.7904 (tt) cc_final: 0.7626 (mp)
REVERT: C  243 MET cc_start: 0.9224 (mtm) cc_final: 0.8960 (ttp)
REVERT: C  246 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8383 (tm-30)
REVERT: C  276 MET cc_start: 0.9014 (ttm) cc_final: 0.8722 (ttm)
REVERT: C  284 MET cc_start: 0.8669 (mtp) cc_final: 0.7846 (tmm)
REVERT: D   97 ILE cc_start: 0.7714 (mt) cc_final: 0.7460 (tt)
REVERT: E  243 MET cc_start: 0.8033 (tpt) cc_final: 0.7431 (tpp)
REVERT: E  246 GLN cc_start: 0.8993 (tt0) cc_final: 0.8720 (tm-30)
REVERT: E  263 MET cc_start: 0.8100 (mmt) cc_final: 0.7709 (tpp)
REVERT: E  276 MET cc_start: 0.9140 (tpp) cc_final: 0.8581 (tpp)
REVERT: E  329 MET cc_start: 0.9107 (tpt) cc_final: 0.8830 (tpt)
REVERT: F   88 PHE cc_start: 0.8592 (t80) cc_final: 0.8344 (t80)
REVERT: G  243 MET cc_start: 0.8642 (ttt) cc_final: 0.7251 (ttt)
REVERT: G  276 MET cc_start: 0.9229 (mtm) cc_final: 0.8714 (tmm)
REVERT: G  287 GLN cc_start: 0.8807 (tt0) cc_final: 0.8453 (tm-30)
REVERT: G  315 GLU cc_start: 0.9282 (pm20) cc_final: 0.9069 (pm20)
REVERT: H   51 THR cc_start: 0.7916 (m) cc_final: 0.7713 (p)
REVERT: H   57 LEU cc_start: 0.8826 (mt) cc_final: 0.8474 (mt)
REVERT: Q  112 MET cc_start: 0.9036 (ttt) cc_final: 0.8830 (mmm)
REVERT: Q  125 ASP cc_start: 0.8630 (t0) cc_final: 0.8335 (t0)
REVERT: Q  130 TYR cc_start: 0.8317 (t80) cc_final: 0.7959 (t80)
REVERT: Q  147 MET cc_start: 0.7707 (ptp) cc_final: 0.7291 (ptp)
REVERT: Q  208 ASP cc_start: 0.8834 (m-30) cc_final: 0.8610 (m-30)
REVERT: Q  256 MET cc_start: 0.8115 (mmm) cc_final: 0.7701 (mmm)
REVERT: Q  330 MET cc_start: 0.8492 (tmm) cc_final: 0.8109 (tmm)
REVERT: Q  386 MET cc_start: 0.8588 (mtt) cc_final: 0.8131 (ttt)
REVERT: Q  445 LEU cc_start: 0.8178 (tp) cc_final: 0.7895 (tp)
REVERT: R   91 MET cc_start: 0.8120 (mtp) cc_final: 0.7405 (mmm)
REVERT: R  191 MET cc_start: 0.6254 (mmm) cc_final: 0.4906 (mmm)
REVERT: R  299 TYR cc_start: 0.8375 (m-80) cc_final: 0.7824 (m-10)
REVERT: R  321 PHE cc_start: 0.9253 (t80) cc_final: 0.8854 (t80)
REVERT: R  322 CYS cc_start: 0.9053 (m) cc_final: 0.8794 (m)
REVERT: R  379 ASP cc_start: 0.7356 (m-30) cc_final: 0.6650 (p0)
REVERT: R  382 LEU cc_start: 0.8606 (tp) cc_final: 0.8310 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.0876
  time to fit residues: 29.7253
Evaluate side-chains
  180 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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**
** A 196 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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.057473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.044093 restraints weight = 75164.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.045474 restraints weight = 43653.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.046439 restraints weight = 29829.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.047048 restraints weight = 22706.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.047415 restraints weight = 18803.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12339  Z= 0.168
  Angle     :  0.660   9.024  16587  Z= 0.341
  Chirality :  0.041   0.197   1793
  Planarity :  0.005   0.116   2094
  Dihedral  :  4.762  20.800   1605
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.22), residues: 1440
  helix:  1.42 (0.16), residues: 1055
  sheet: -4.22 (0.69), residues: 17
  loop : -1.48 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 252 
 TYR   0.024   0.002   TYR A 289 
 PHE   0.023   0.002   PHE H  88 
 TRP   0.014   0.001   TRP A 255 
 HIS   0.004   0.001   HIS G 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12339)
  covalent geometry    : angle       0.65965 (16587)
  hydrogen bonds       : bond        0.03796 (  785)
  hydrogen bonds       : angle       4.21211 ( 2331)

*********************** 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
  213 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.430 
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  218 GLU cc_start: 0.9118 (pt0) cc_final: 0.8576 (pm20)
REVERT: A  243 MET cc_start: 0.8644 (ttm) cc_final: 0.8331 (ttm)
REVERT: A  263 MET cc_start: 0.9172 (mmm) cc_final: 0.8966 (mmm)
REVERT: A  267 THR cc_start: 0.8689 (m) cc_final: 0.8420 (m)
REVERT: A  335 ARG cc_start: 0.7868 (tmt170) cc_final: 0.7495 (tpt90)
REVERT: A  339 GLN cc_start: 0.6886 (tt0) cc_final: 0.6593 (pt0)
REVERT: B   80 VAL cc_start: 0.9292 (m) cc_final: 0.9055 (m)
REVERT: B   83 LEU cc_start: 0.8972 (mm) cc_final: 0.8628 (mp)
REVERT: B   91 LEU cc_start: 0.7929 (tt) cc_final: 0.7652 (mp)
REVERT: C  243 MET cc_start: 0.9258 (mtm) cc_final: 0.8948 (ttp)
REVERT: C  246 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: C  259 SER cc_start: 0.8201 (t) cc_final: 0.7951 (t)
REVERT: C  276 MET cc_start: 0.8976 (ttm) cc_final: 0.8656 (ttm)
REVERT: C  284 MET cc_start: 0.8740 (mtp) cc_final: 0.7891 (tmm)
REVERT: C  326 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8589 (tp-100)
REVERT: D   97 ILE cc_start: 0.7786 (mt) cc_final: 0.7427 (tt)
REVERT: E  243 MET cc_start: 0.8082 (tpt) cc_final: 0.7495 (tpp)
REVERT: E  246 GLN cc_start: 0.8991 (tt0) cc_final: 0.8744 (tm-30)
REVERT: E  268 TYR cc_start: 0.8564 (t80) cc_final: 0.8282 (t80)
REVERT: E  276 MET cc_start: 0.9081 (tpp) cc_final: 0.8488 (mmt)
REVERT: E  329 MET cc_start: 0.8998 (tpt) cc_final: 0.8754 (tpt)
REVERT: F   71 PHE cc_start: 0.8141 (m-80) cc_final: 0.7819 (m-80)
REVERT: F   88 PHE cc_start: 0.8623 (t80) cc_final: 0.8369 (t80)
REVERT: G  243 MET cc_start: 0.8596 (ttt) cc_final: 0.7984 (ttt)
REVERT: G  276 MET cc_start: 0.9311 (mtm) cc_final: 0.8698 (tmm)
REVERT: G  287 GLN cc_start: 0.8836 (tt0) cc_final: 0.8442 (tm-30)
REVERT: G  315 GLU cc_start: 0.9310 (pm20) cc_final: 0.9104 (pm20)
REVERT: H   51 THR cc_start: 0.8226 (m) cc_final: 0.8022 (p)
REVERT: H   57 LEU cc_start: 0.8828 (mt) cc_final: 0.8513 (mt)
REVERT: H   67 LEU cc_start: 0.8975 (mt) cc_final: 0.8312 (pt)
REVERT: Q  125 ASP cc_start: 0.8655 (t0) cc_final: 0.8381 (t0)
REVERT: Q  130 TYR cc_start: 0.8374 (t80) cc_final: 0.7951 (t80)
REVERT: Q  147 MET cc_start: 0.7928 (ptp) cc_final: 0.7377 (ptp)
REVERT: Q  208 ASP cc_start: 0.8876 (m-30) cc_final: 0.8646 (m-30)
REVERT: Q  229 MET cc_start: 0.8547 (mmp) cc_final: 0.8052 (mmp)
REVERT: Q  256 MET cc_start: 0.8294 (mmm) cc_final: 0.7831 (mmm)
REVERT: Q  330 MET cc_start: 0.8657 (tmm) cc_final: 0.8238 (tmm)
REVERT: Q  386 MET cc_start: 0.8592 (mtt) cc_final: 0.8127 (ttt)
REVERT: Q  445 LEU cc_start: 0.8237 (tp) cc_final: 0.7941 (tp)
REVERT: R  191 MET cc_start: 0.6415 (mmm) cc_final: 0.5261 (mmm)
REVERT: R  299 TYR cc_start: 0.8480 (m-80) cc_final: 0.7912 (m-10)
REVERT: R  321 PHE cc_start: 0.9103 (t80) cc_final: 0.8712 (t80)
REVERT: R  322 CYS cc_start: 0.9058 (m) cc_final: 0.8773 (m)
REVERT: R  382 LEU cc_start: 0.8876 (tp) cc_final: 0.8600 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0878
  time to fit residues: 28.2193
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  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 114 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   chunk 88 optimal weight:    0.7980
   chunk 108 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 430 ASN
R 235 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.058307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.044933 restraints weight = 74928.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.046386 restraints weight = 43275.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.047350 restraints weight = 29334.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.047940 restraints weight = 22251.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.048405 restraints weight = 18496.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.4925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12339  Z= 0.126
  Angle     :  0.640  10.916  16587  Z= 0.326
  Chirality :  0.041   0.189   1793
  Planarity :  0.004   0.098   2094
  Dihedral  :  4.653  20.435   1605
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.22), residues: 1440
  helix:  1.45 (0.16), residues: 1063
  sheet: -4.25 (0.67), residues: 17
  loop : -1.57 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 252 
 TYR   0.020   0.001   TYR E 268 
 PHE   0.027   0.001   PHE H  88 
 TRP   0.011   0.001   TRP C 256 
 HIS   0.004   0.001   HIS Q 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (12339)
  covalent geometry    : angle       0.64019 (16587)
  hydrogen bonds       : bond        0.03618 (  785)
  hydrogen bonds       : angle       4.10485 ( 2331)

********************** 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
  217 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.604 
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  214 LEU cc_start: 0.9326 (tp) cc_final: 0.8981 (tp)
REVERT: A  218 GLU cc_start: 0.9090 (pt0) cc_final: 0.8689 (pm20)
REVERT: A  263 MET cc_start: 0.9116 (mmm) cc_final: 0.8911 (mmm)
REVERT: A  267 THR cc_start: 0.8666 (m) cc_final: 0.8407 (m)
REVERT: A  279 TYR cc_start: 0.7764 (t80) cc_final: 0.6827 (t80)
REVERT: A  335 ARG cc_start: 0.7883 (tmt170) cc_final: 0.7586 (tpt90)
REVERT: A  339 GLN cc_start: 0.6866 (tt0) cc_final: 0.6580 (pt0)
REVERT: B   80 VAL cc_start: 0.9291 (m) cc_final: 0.9051 (m)
REVERT: B   83 LEU cc_start: 0.8960 (mm) cc_final: 0.8597 (mp)
REVERT: B   91 LEU cc_start: 0.7901 (tt) cc_final: 0.7642 (mt)
REVERT: C  246 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: C  276 MET cc_start: 0.8976 (ttm) cc_final: 0.8447 (tmm)
REVERT: C  278 MET cc_start: 0.7558 (mmt) cc_final: 0.7025 (mmp)
REVERT: C  284 MET cc_start: 0.8733 (mtp) cc_final: 0.7863 (tmm)
REVERT: D   97 ILE cc_start: 0.7710 (mt) cc_final: 0.7386 (tt)
REVERT: E  246 GLN cc_start: 0.9040 (tt0) cc_final: 0.8798 (tm-30)
REVERT: E  263 MET cc_start: 0.8236 (mmm) cc_final: 0.7982 (tpp)
REVERT: E  276 MET cc_start: 0.9074 (tpp) cc_final: 0.8332 (tpp)
REVERT: E  329 MET cc_start: 0.9103 (tpt) cc_final: 0.8846 (tpt)
REVERT: F   71 PHE cc_start: 0.8188 (m-80) cc_final: 0.7807 (m-80)
REVERT: F   88 PHE cc_start: 0.8615 (t80) cc_final: 0.8368 (t80)
REVERT: G  243 MET cc_start: 0.8627 (ttt) cc_final: 0.7437 (ttt)
REVERT: G  276 MET cc_start: 0.9288 (mtm) cc_final: 0.8699 (tmm)
REVERT: G  287 GLN cc_start: 0.8834 (tt0) cc_final: 0.8485 (tm-30)
REVERT: G  315 GLU cc_start: 0.9347 (pm20) cc_final: 0.9145 (pm20)
REVERT: H   57 LEU cc_start: 0.8801 (mt) cc_final: 0.8437 (mt)
REVERT: H   67 LEU cc_start: 0.8981 (mt) cc_final: 0.8344 (pt)
REVERT: Q  125 ASP cc_start: 0.8576 (t0) cc_final: 0.8319 (t0)
REVERT: Q  130 TYR cc_start: 0.8302 (t80) cc_final: 0.7890 (t80)
REVERT: Q  147 MET cc_start: 0.7825 (ptp) cc_final: 0.7338 (ptp)
REVERT: Q  229 MET cc_start: 0.8610 (mmp) cc_final: 0.8132 (mmp)
REVERT: Q  256 MET cc_start: 0.8225 (mmm) cc_final: 0.7759 (mmm)
REVERT: Q  330 MET cc_start: 0.8510 (tmm) cc_final: 0.8139 (tmm)
REVERT: Q  386 MET cc_start: 0.8609 (mtt) cc_final: 0.8133 (ttt)
REVERT: Q  445 LEU cc_start: 0.8196 (tp) cc_final: 0.7919 (tp)
REVERT: R  191 MET cc_start: 0.6477 (mmm) cc_final: 0.5461 (mmm)
REVERT: R  299 TYR cc_start: 0.8442 (m-80) cc_final: 0.7862 (m-10)
REVERT: R  321 PHE cc_start: 0.9256 (t80) cc_final: 0.8859 (t80)
REVERT: R  322 CYS cc_start: 0.9050 (m) cc_final: 0.8776 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.0834
  time to fit residues: 27.3800
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  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 130 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0370
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0000
   chunk 68 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    1.4066

-------------------------------------------------------------------------------
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**
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 HIS
** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 235 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.058676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.045346 restraints weight = 74232.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.046799 restraints weight = 42663.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.047795 restraints weight = 28865.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.048369 restraints weight = 21771.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.048842 restraints weight = 18125.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.5075

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= 0.123
  Angle     :  0.638  11.214  16587  Z= 0.322
  Chirality :  0.041   0.182   1793
  Planarity :  0.004   0.072   2094
  Dihedral  :  4.637  20.504   1605
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.22), residues: 1440
  helix:  1.44 (0.16), residues: 1061
  sheet: -4.29 (0.67), residues: 17
  loop : -1.52 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 201 
 TYR   0.019   0.001   TYR E 268 
 PHE   0.028   0.001   PHE R 252 
 TRP   0.012   0.001   TRP C 256 
 HIS   0.004   0.001   HIS Q 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12339)
  covalent geometry    : angle       0.63809 (16587)
  hydrogen bonds       : bond        0.03593 (  785)
  hydrogen bonds       : angle       4.05083 ( 2331)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1702.50 seconds
wall clock time: 30 minutes 19.01 seconds (1819.01 seconds total)