Starting phenix.real_space_refine
on Sat Oct 11 08:08:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uop_42435/10_2025/8uop_42435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uop_42435/10_2025/8uop_42435.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uop_42435/10_2025/8uop_42435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uop_42435/10_2025/8uop_42435.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uop_42435/10_2025/8uop_42435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uop_42435/10_2025/8uop_42435.map"
  }
  resolution = 3.8
  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=  -0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4182      2.51       5
     N    1122      2.21       5
     O    1318      1.98       5
     H    6544      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13188
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6594
          Classifications: {'peptide': 436}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "B"
      Number of atoms: 6594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6594
          Classifications: {'peptide': 436}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
  Time building chain proxies: 2.91, per 1000 atoms: 0.22
  Number of scatterers: 13188
  At special positions: 0
  Unit cell: (99.176, 76.538, 89.474, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     O    1318      8.00
     N    1122      7.00
     C    4182      6.00
     H    6544      1.00
    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: 1.08
  Conformation dependent library (CDL) restraints added in 384.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      40.9% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 73
    Processing helix  chain 'A' and resid 74 through 78
    Processing helix  chain 'A' and resid 86 through 92
    Processing helix  chain 'A' and resid 93 through 99
      removed outlier: 4.030A  pdb=" N   LEU A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 120
      removed outlier: 3.731A  pdb=" N   VAL A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 126
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 153 through 156
      removed outlier: 3.768A  pdb=" N   SER A 156 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 153 through 156'
    Processing helix  chain 'A' and resid 176 through 197
      removed outlier: 4.340A  pdb=" N   ARG A 180 " --> pdb=" O   LYS A 176 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   VAL A 185 " --> pdb=" O   TRP A 181 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   PHE A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   HIS A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA A 188 " --> pdb=" O   GLU A 184 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ILE A 192 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   GLU A 195 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 230
      removed outlier: 3.892A  pdb=" N   LEU A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 271 through 286
      removed outlier: 4.555A  pdb=" N   VAL A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   ASP A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TYR A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 279 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ASN A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   LYS A 285 " --> pdb=" O   GLU A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 325 through 335
      removed outlier: 3.618A  pdb=" N   GLU A 335 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 349
    Processing helix  chain 'A' and resid 350 through 364
    Processing helix  chain 'A' and resid 380 through 389
      removed outlier: 3.826A  pdb=" N   ASP A 384 " --> pdb=" O   SER A 380 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ILE A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   ALA A 386 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 416
      removed outlier: 4.837A  pdb=" N   LYS A 407 " --> pdb=" O   ASP A 403 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TYR A 408 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ARG A 413 " --> pdb=" O   ASN A 409 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE A 414 " --> pdb=" O   GLN A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'B' and resid 64 through 73
      removed outlier: 3.856A  pdb=" N   ASN B  70 " --> pdb=" O   LYS B  66 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   VAL B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 99
      removed outlier: 3.538A  pdb=" N   ILE B  90 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ALA B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   MET B  94 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE B  95 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ALA B  96 " --> pdb=" O   ARG B  92 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LEU B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASP B  98 " --> pdb=" O   MET B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 124
      removed outlier: 3.656A  pdb=" N   SER B 115 " --> pdb=" O   ILE B 111 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ALA B 122 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   ASP B 124 " --> pdb=" O   ARG B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 134
      removed outlier: 4.098A  pdb=" N   LEU B 134 " --> pdb=" O   TYR B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 156
    Processing helix  chain 'B' and resid 174 through 188
      removed outlier: 5.006A  pdb=" N   ARG B 180 " --> pdb=" O   LYS B 176 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   TRP B 181 " --> pdb=" O   GLU B 177 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ALA B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 196
    Processing helix  chain 'B' and resid 214 through 218
    Processing helix  chain 'B' and resid 219 through 228
      removed outlier: 3.619A  pdb=" N   LYS B 224 " --> pdb=" O   GLU B 220 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA B 225 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 285
      removed outlier: 3.803A  pdb=" N   LEU B 282 " --> pdb=" O   TYR B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 3.791A  pdb=" N   VAL B 305 " --> pdb=" O   ASP B 301 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 301 through 306'
    Processing helix  chain 'B' and resid 325 through 336
      removed outlier: 4.176A  pdb=" N   ILE B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 348
      removed outlier: 3.555A  pdb=" N   ILE B 348 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 363
    Processing helix  chain 'B' and resid 380 through 389
    Processing helix  chain 'B' and resid 401 through 419
      removed outlier: 3.640A  pdb=" N   LYS B 407 " --> pdb=" O   ASP B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 430
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14
      removed outlier: 3.641A  pdb=" N   ASN A  18 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   LEU A  21 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 151
      removed outlier: 6.480A  pdb=" N   ASN A 148 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   ILE A 167 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ILE A 150 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLU A 164 " --> pdb=" O   ASP A 243 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   ILE A 240 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ILE A 291 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   PHE A 242 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ILE A 289 " --> pdb=" O   GLN A 315 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   VAL A 317 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   ILE A 291 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LEU A 342 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLY A 318 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ALA A 368 " --> pdb=" O   GLN A 393 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   LYS A 395 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL A 370 " --> pdb=" O   LYS A 395 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   THR A 144 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 12
    Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 243
      removed outlier: 4.523A  pdb=" N   MET B 239 " --> pdb=" O   MET B 168 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   MET B 168 " --> pdb=" O   MET B 239 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLU B 164 " --> pdb=" O   ASP B 243 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   PHE B 165 " --> pdb=" O   ILE B 149 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN B 393 " --> pdb=" O   ALA B 368 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE B 341 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   SER B 371 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 290 through 292
      removed outlier: 6.673A  pdb=" N   ILE B 291 " --> pdb=" O   VAL B 317 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    206 hydrogen bonds defined for protein.
    555 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: 2.81

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6542
        1.03 -     1.23: 6
        1.23 -     1.42: 2788
        1.42 -     1.62: 3916
        1.62 -     1.81: 42
  Bond restraints: 13294
  Sorted by residual:
  bond pdb=" C   TYR A 286 "
       pdb=" N   PRO A 287 "
    ideal  model  delta    sigma   weight residual
    1.332  1.363 -0.031 1.34e-02 5.57e+03 5.46e+00
  bond pdb=" CA  TYR A 286 "
       pdb=" CB  TYR A 286 "
    ideal  model  delta    sigma   weight residual
    1.528  1.559 -0.031 1.41e-02 5.03e+03 4.91e+00
  bond pdb=" CB  ASP B 299 "
       pdb=" CG  ASP B 299 "
    ideal  model  delta    sigma   weight residual
    1.516  1.571 -0.055 2.50e-02 1.60e+03 4.76e+00
  bond pdb=" CA  ASN A 236 "
       pdb=" CB  ASN A 236 "
    ideal  model  delta    sigma   weight residual
    1.530  1.560 -0.030 1.39e-02 5.18e+03 4.60e+00
  bond pdb=" N   MET B 168 "
       pdb=" CA  MET B 168 "
    ideal  model  delta    sigma   weight residual
    1.453  1.469 -0.015 9.20e-03 1.18e+04 2.83e+00
  ... (remaining 13289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 23444
        1.95 -     3.89: 529
        3.89 -     5.84: 46
        5.84 -     7.79: 2
        7.79 -     9.73: 1
  Bond angle restraints: 24022
  Sorted by residual:
  angle pdb=" N   ASP B   6 "
        pdb=" CA  ASP B   6 "
        pdb=" C   ASP B   6 "
      ideal   model   delta    sigma   weight residual
     108.46  114.83   -6.37 1.51e+00 4.39e-01 1.78e+01
  angle pdb=" N   VAL B 421 "
        pdb=" CA  VAL B 421 "
        pdb=" C   VAL B 421 "
      ideal   model   delta    sigma   weight residual
     106.21  110.24   -4.03 1.07e+00 8.73e-01 1.42e+01
  angle pdb=" N   ALA B  48 "
        pdb=" CA  ALA B  48 "
        pdb=" C   ALA B  48 "
      ideal   model   delta    sigma   weight residual
     110.70  105.07    5.63 1.55e+00 4.16e-01 1.32e+01
  angle pdb=" N   LEU B  97 "
        pdb=" CA  LEU B  97 "
        pdb=" C   LEU B  97 "
      ideal   model   delta    sigma   weight residual
     113.18  108.37    4.81 1.33e+00 5.65e-01 1.31e+01
  angle pdb=" N   THR B 200 "
        pdb=" CA  THR B 200 "
        pdb=" C   THR B 200 "
      ideal   model   delta    sigma   weight residual
     107.57  114.21   -6.64 1.94e+00 2.66e-01 1.17e+01
  ... (remaining 24017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 5396
       17.46 -    34.91: 568
       34.91 -    52.37: 182
       52.37 -    69.83: 55
       69.83 -    87.29: 11
  Dihedral angle restraints: 6212
    sinusoidal: 3390
      harmonic: 2822
  Sorted by residual:
  dihedral pdb=" CA  GLU A 235 "
           pdb=" C   GLU A 235 "
           pdb=" N   ASN A 236 "
           pdb=" CA  ASN A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.98   30.02     0      5.00e+00 4.00e-02 3.60e+01
  dihedral pdb=" CA  ALA B 228 "
           pdb=" C   ALA B 228 "
           pdb=" N   ALA B 229 "
           pdb=" CA  ALA B 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.71   29.29     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  ALA B 225 "
           pdb=" C   ALA B 225 "
           pdb=" N   ILE B 226 "
           pdb=" CA  ILE B 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.57   26.43     0      5.00e+00 4.00e-02 2.79e+01
  ... (remaining 6209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 646
       0.036 -    0.072: 267
       0.072 -    0.109: 87
       0.109 -    0.145: 23
       0.145 -    0.181: 3
  Chirality restraints: 1026
  Sorted by residual:
  chirality pdb=" CB  VAL A 219 "
            pdb=" CA  VAL A 219 "
            pdb=" CG1 VAL A 219 "
            pdb=" CG2 VAL A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.18e-01
  chirality pdb=" CG  LEU B 198 "
            pdb=" CB  LEU B 198 "
            pdb=" CD1 LEU B 198 "
            pdb=" CD2 LEU B 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  ILE A 288 "
            pdb=" N   ILE A 288 "
            pdb=" C   ILE A 288 "
            pdb=" CB  ILE A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1023 not shown)

  Planarity restraints: 2046
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 225 "    0.013 2.00e-02 2.50e+03   2.56e-02 6.53e+00
        pdb=" C   ALA B 225 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ALA B 225 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE B 226 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 286 "    0.020 2.00e-02 2.50e+03   1.21e-02 4.39e+00
        pdb=" CG  TYR A 286 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 286 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 286 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 286 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 286 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 286 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 286 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 286 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 286 "   -0.009 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 286 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 286 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 193 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   LEU B 193 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LEU B 193 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LYS B 194 "    0.011 2.00e-02 2.50e+03
  ... (remaining 2043 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 348
        2.09 -     2.72: 22698
        2.72 -     3.34: 37656
        3.34 -     3.97: 45929
        3.97 -     4.60: 72127
  Nonbonded interactions: 178758
  Sorted by model distance:
  nonbonded pdb=" HH  TYR B 257 "
            pdb=" OD2 ASP B 299 "
     model   vdw
     1.459 2.450
  nonbonded pdb=" H   ASP B 293 "
            pdb=" O   VAL B 317 "
     model   vdw
     1.486 2.450
  nonbonded pdb=" OG  SER B 246 "
            pdb=" H   MET B 295 "
     model   vdw
     1.530 2.450
  nonbonded pdb=" O   ASN B 298 "
            pdb=" H   TRP B 300 "
     model   vdw
     1.555 2.450
  nonbonded pdb="HH11 ARG B 180 "
            pdb=" OE2 GLU B 184 "
     model   vdw
     1.573 2.450
  ... (remaining 178753 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.750
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1503
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6750  Z= 0.245
  Angle     :  0.905   9.735   9128  Z= 0.547
  Chirality :  0.045   0.181   1026
  Planarity :  0.005   0.055   1198
  Dihedral  : 16.453  87.286   2470
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.69 %
    Allowed  : 15.67 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 17.45 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -3.60 (0.25), residues: 868
  helix: -1.37 (0.30), residues: 264
  sheet: -2.50 (0.61), residues: 64
  loop : -3.09 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 309 
 TYR   0.034   0.003   TYR A 286 
 PHE   0.018   0.003   PHE A 175 
 TRP   0.028   0.005   TRP A 300 
 HIS   0.009   0.002   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 6750)
  covalent geometry    : angle       0.90511 ( 9128)
  hydrogen bonds       : bond        0.18619 (  206)
  hydrogen bonds       : angle       8.03634 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.339 
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  131 TYR cc_start: 0.0860 (p90) cc_final: 0.0131 (p90)
REVERT: A  359 GLU cc_start: 0.1655 (tm-30) cc_final: -0.0746 (mt-10)
REVERT: B    6 ASP cc_start: 0.5409 (p0) cc_final: 0.5123 (p0)
REVERT: B   92 ARG cc_start: 0.3431 (mmt180) cc_final: 0.2180 (tpt90)
REVERT: B  239 MET cc_start: 0.2235 (mmp) cc_final: 0.1922 (mmt)
REVERT: B  360 MET cc_start: 0.0955 (tpt) cc_final: 0.0246 (mtp)
  outliers start: 5
  outliers final: 2
  residues processed: 95
  average time/residue: 0.1802
  time to fit residues: 23.0682
Evaluate side-chains
  68 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain B residue  316 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 187 HIS
** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5316 r_free = 0.5316 target = 0.342587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5276 r_free = 0.5276 target = 0.338050 restraints weight = 41749.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5290 r_free = 0.5290 target = 0.339904 restraints weight = 25766.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5298 r_free = 0.5298 target = 0.340827 restraints weight = 15132.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5306 r_free = 0.5306 target = 0.341797 restraints weight = 8632.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.5309 r_free = 0.5309 target = 0.342107 restraints weight = 4285.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.5311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2211
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.105   6750  Z= 0.275
  Angle     :  0.862  10.828   9128  Z= 0.467
  Chirality :  0.047   0.177   1026
  Planarity :  0.006   0.055   1198
  Dihedral  :  7.644  51.499    950
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 13.94 %
    Favored  : 85.60 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.60 %
    Favored  : 78.59 %
  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: -3.75 (0.25), residues: 868
  helix: -1.55 (0.27), residues: 273
  sheet: -2.88 (0.59), residues: 68
  loop : -3.12 (0.24), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  85 
 TYR   0.022   0.002   TYR A 278 
 PHE   0.021   0.002   PHE B 165 
 TRP   0.015   0.003   TRP A 303 
 HIS   0.012   0.003   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 6750)
  covalent geometry    : angle       0.86150 ( 9128)
  hydrogen bonds       : bond        0.05112 (  206)
  hydrogen bonds       : angle       6.72471 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 ILE cc_start: 0.3062 (OUTLIER) cc_final: 0.2407 (mm)
REVERT: A   94 MET cc_start: 0.3276 (tpp) cc_final: 0.2731 (ttm)
REVERT: A  131 TYR cc_start: 0.1276 (p90) cc_final: 0.0695 (p90)
REVERT: A  376 GLU cc_start: 0.0929 (mm-30) cc_final: 0.0222 (mp0)
REVERT: B    6 ASP cc_start: 0.6769 (p0) cc_final: 0.6122 (p0)
REVERT: B  239 MET cc_start: 0.2984 (mmp) cc_final: 0.2031 (mmp)
REVERT: B  360 MET cc_start: 0.1153 (tpt) cc_final: 0.0239 (mtp)
  outliers start: 26
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1309
  time to fit residues: 17.8466
Evaluate side-chains
  75 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    0 HIS
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  367 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0870
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.7964

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN
B 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5327 r_free = 0.5327 target = 0.341696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.5267 r_free = 0.5267 target = 0.335115 restraints weight = 41426.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.337297 restraints weight = 23985.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5299 r_free = 0.5299 target = 0.338559 restraints weight = 14572.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.5307 r_free = 0.5307 target = 0.339489 restraints weight = 9407.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.340200 restraints weight = 6196.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.5318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2277
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6750  Z= 0.195
  Angle     :  0.697   7.059   9128  Z= 0.381
  Chirality :  0.044   0.163   1026
  Planarity :  0.004   0.043   1198
  Dihedral  :  7.245  55.689    950
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 13.36 %
    Favored  : 86.29 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 18.33 %
    Favored  : 77.13 %
  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: -3.66 (0.26), residues: 868
  helix: -1.20 (0.29), residues: 263
  sheet: -3.09 (0.53), residues: 83
  loop : -3.14 (0.24), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  85 
 TYR   0.021   0.002   TYR A 278 
 PHE   0.018   0.002   PHE B 165 
 TRP   0.011   0.002   TRP B 303 
 HIS   0.007   0.002   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6750)
  covalent geometry    : angle       0.69660 ( 9128)
  hydrogen bonds       : bond        0.04220 (  206)
  hydrogen bonds       : angle       6.43427 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 62
  time to evaluate  : 0.353 
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   79 ILE cc_start: 0.2720 (OUTLIER) cc_final: 0.2161 (mm)
REVERT: A  131 TYR cc_start: 0.1345 (p90) cc_final: 0.0828 (p90)
REVERT: A  166 MET cc_start: 0.1367 (mmm) cc_final: 0.0374 (mpp)
REVERT: A  235 GLU cc_start: 0.0906 (OUTLIER) cc_final: -0.1084 (pt0)
REVERT: A  259 TYR cc_start: -0.0583 (OUTLIER) cc_final: -0.0951 (t80)
REVERT: A  376 GLU cc_start: 0.1187 (mm-30) cc_final: 0.0376 (mp0)
REVERT: B  239 MET cc_start: 0.3174 (mmp) cc_final: 0.2282 (mmp)
  outliers start: 31
  outliers final: 18
  residues processed: 87
  average time/residue: 0.1433
  time to fit residues: 18.0981
Evaluate side-chains
  80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain B residue    6 ASP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 30 optimal weight:    0.2980
   chunk 15 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 43 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 58 optimal weight:    9.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 325 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5317 r_free = 0.5317 target = 0.341472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.5251 r_free = 0.5251 target = 0.334012 restraints weight = 41085.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.5273 r_free = 0.5273 target = 0.336496 restraints weight = 23387.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5287 r_free = 0.5287 target = 0.338077 restraints weight = 14028.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.5296 r_free = 0.5296 target = 0.339142 restraints weight = 8693.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.339880 restraints weight = 5481.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.5303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2220
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6750  Z= 0.127
  Angle     :  0.590   5.410   9128  Z= 0.323
  Chirality :  0.042   0.148   1026
  Planarity :  0.004   0.038   1198
  Dihedral  :  6.706  59.500    950
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 11.75 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.50 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.26), residues: 868
  helix: -0.86 (0.31), residues: 257
  sheet: -2.76 (0.51), residues: 89
  loop : -3.08 (0.24), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 254 
 TYR   0.019   0.001   TYR A 278 
 PHE   0.015   0.001   PHE B 242 
 TRP   0.004   0.001   TRP B 303 
 HIS   0.007   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6750)
  covalent geometry    : angle       0.59039 ( 9128)
  hydrogen bonds       : bond        0.03458 (  206)
  hydrogen bonds       : angle       5.95227 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.3088 (ptp) cc_final: 0.2821 (ptp)
REVERT: A   79 ILE cc_start: 0.2663 (OUTLIER) cc_final: 0.2156 (mm)
REVERT: A   94 MET cc_start: 0.3181 (tpp) cc_final: 0.2721 (ttm)
REVERT: A  131 TYR cc_start: 0.1311 (p90) cc_final: 0.0779 (p90)
REVERT: A  162 PHE cc_start: 0.2053 (m-80) cc_final: 0.1516 (m-80)
REVERT: A  166 MET cc_start: 0.1405 (mmm) cc_final: 0.0447 (mpp)
REVERT: A  259 TYR cc_start: -0.0653 (OUTLIER) cc_final: -0.0971 (t80)
REVERT: A  376 GLU cc_start: 0.1078 (mm-30) cc_final: 0.0084 (mp0)
REVERT: B  239 MET cc_start: 0.3225 (mmp) cc_final: 0.2254 (mmt)
REVERT: B  360 MET cc_start: 0.1349 (tpt) cc_final: -0.0284 (mtt)
  outliers start: 24
  outliers final: 15
  residues processed: 80
  average time/residue: 0.1409
  time to fit residues: 16.6689
Evaluate side-chains
  76 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  316 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 25 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
A 315 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5297 r_free = 0.5297 target = 0.338812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.5237 r_free = 0.5237 target = 0.332336 restraints weight = 41606.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5252 r_free = 0.5252 target = 0.334128 restraints weight = 25398.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.335427 restraints weight = 15865.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5273 r_free = 0.5273 target = 0.336296 restraints weight = 10561.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.5278 r_free = 0.5278 target = 0.336938 restraints weight = 7299.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.5282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2450
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   6750  Z= 0.219
  Angle     :  0.728   7.101   9128  Z= 0.399
  Chirality :  0.045   0.177   1026
  Planarity :  0.005   0.050   1198
  Dihedral  :  7.387  54.625    950
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 14.29 %
    Favored  : 85.25 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 18.77 %
    Favored  : 75.37 %
  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: -3.69 (0.25), residues: 868
  helix: -1.15 (0.30), residues: 257
  sheet: -3.07 (0.51), residues: 85
  loop : -3.20 (0.24), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  85 
 TYR   0.021   0.002   TYR A 278 
 PHE   0.023   0.002   PHE B 242 
 TRP   0.009   0.002   TRP A 303 
 HIS   0.006   0.002   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 6750)
  covalent geometry    : angle       0.72782 ( 9128)
  hydrogen bonds       : bond        0.04027 (  206)
  hydrogen bonds       : angle       6.41988 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 62
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 ILE cc_start: 0.2651 (OUTLIER) cc_final: 0.2278 (tp)
REVERT: A  166 MET cc_start: 0.1578 (mmm) cc_final: 0.0367 (mpp)
REVERT: A  235 GLU cc_start: 0.1109 (OUTLIER) cc_final: -0.0785 (pt0)
REVERT: A  259 TYR cc_start: 0.0089 (OUTLIER) cc_final: -0.0572 (t80)
REVERT: A  376 GLU cc_start: 0.1779 (mm-30) cc_final: 0.0721 (mt-10)
REVERT: B   85 ARG cc_start: 0.1502 (ttp-170) cc_final: 0.0666 (ttm170)
REVERT: B   94 MET cc_start: 0.5457 (mmp) cc_final: 0.5048 (mmp)
REVERT: B  239 MET cc_start: 0.3339 (mmp) cc_final: 0.2243 (mmt)
REVERT: B  286 TYR cc_start: -0.1743 (OUTLIER) cc_final: -0.2186 (t80)
REVERT: B  360 MET cc_start: 0.1463 (tpt) cc_final: 0.0127 (mtt)
  outliers start: 40
  outliers final: 28
  residues processed: 93
  average time/residue: 0.1638
  time to fit residues: 21.3034
Evaluate side-chains
  92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain B residue    6 ASP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  366 TYR
Chi-restraints excluded: chain B residue  367 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5290 r_free = 0.5290 target = 0.338354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.5237 r_free = 0.5237 target = 0.332170 restraints weight = 41611.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5247 r_free = 0.5247 target = 0.333448 restraints weight = 25524.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.334596 restraints weight = 16696.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.5264 r_free = 0.5264 target = 0.335496 restraints weight = 11394.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.5270 r_free = 0.5270 target = 0.336185 restraints weight = 8112.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.5273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2474
moved from start:          0.5632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6750  Z= 0.195
  Angle     :  0.681   6.338   9128  Z= 0.375
  Chirality :  0.044   0.166   1026
  Planarity :  0.005   0.051   1198
  Dihedral  :  7.277  51.943    950
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 14.17 %
    Favored  : 85.60 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 21.11 %
    Favored  : 73.75 %
  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: -3.70 (0.25), residues: 868
  helix: -1.30 (0.29), residues: 263
  sheet: -2.89 (0.57), residues: 75
  loop : -3.19 (0.24), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 313 
 TYR   0.017   0.002   TYR A 278 
 PHE   0.021   0.002   PHE B 165 
 TRP   0.007   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 6750)
  covalent geometry    : angle       0.68141 ( 9128)
  hydrogen bonds       : bond        0.03797 (  206)
  hydrogen bonds       : angle       6.30325 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 57
  time to evaluate  : 0.293 
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: A   82 TYR cc_start: 0.2841 (OUTLIER) cc_final: 0.1776 (t80)
REVERT: A  166 MET cc_start: 0.1539 (mmm) cc_final: 0.0443 (mpp)
REVERT: A  235 GLU cc_start: 0.1167 (OUTLIER) cc_final: -0.2388 (mt-10)
REVERT: A  259 TYR cc_start: 0.0192 (OUTLIER) cc_final: -0.0455 (t80)
REVERT: A  376 GLU cc_start: 0.1087 (mm-30) cc_final: 0.0272 (mt-10)
REVERT: B   85 ARG cc_start: 0.1454 (ttp-170) cc_final: -0.0210 (ttp-170)
REVERT: B   94 MET cc_start: 0.5293 (mmp) cc_final: 0.5036 (mmp)
REVERT: B  212 PHE cc_start: 0.2560 (OUTLIER) cc_final: 0.1791 (t80)
REVERT: B  239 MET cc_start: 0.3552 (mmp) cc_final: 0.2343 (mmt)
REVERT: B  286 TYR cc_start: -0.1817 (OUTLIER) cc_final: -0.2158 (t80)
REVERT: B  360 MET cc_start: 0.1512 (tpt) cc_final: 0.0021 (mtt)
  outliers start: 35
  outliers final: 25
  residues processed: 85
  average time/residue: 0.1435
  time to fit residues: 17.5436
Evaluate side-chains
  84 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 54
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  366 TYR
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  421 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B   0 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5278 r_free = 0.5278 target = 0.336637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5176 r_free = 0.5176 target = 0.324571 restraints weight = 40211.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5217 r_free = 0.5217 target = 0.329631 restraints weight = 30708.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5236 r_free = 0.5236 target = 0.332000 restraints weight = 13323.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.5249 r_free = 0.5249 target = 0.333742 restraints weight = 8165.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.5253 r_free = 0.5253 target = 0.334134 restraints weight = 6064.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.5257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2542
moved from start:          0.6451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   6750  Z= 0.268
  Angle     :  0.815   8.312   9128  Z= 0.448
  Chirality :  0.047   0.216   1026
  Planarity :  0.006   0.056   1198
  Dihedral  :  8.053  52.714    950
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 20.70
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 16.36 %
    Favored  : 83.29 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 20.09 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -4.04 (0.25), residues: 868
  helix: -1.50 (0.29), residues: 242
  sheet: -3.08 (0.53), residues: 85
  loop : -3.38 (0.23), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 313 
 TYR   0.020   0.002   TYR A 278 
 PHE   0.025   0.003   PHE B 165 
 TRP   0.011   0.002   TRP A 181 
 HIS   0.008   0.002   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 6750)
  covalent geometry    : angle       0.81485 ( 9128)
  hydrogen bonds       : bond        0.04460 (  206)
  hydrogen bonds       : angle       6.84371 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 53
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TYR cc_start: 0.3357 (OUTLIER) cc_final: 0.2102 (t80)
REVERT: A  235 GLU cc_start: 0.1056 (OUTLIER) cc_final: -0.0438 (pt0)
REVERT: A  259 TYR cc_start: -0.0209 (OUTLIER) cc_final: -0.0738 (t80)
REVERT: A  435 LYS cc_start: 0.3405 (OUTLIER) cc_final: 0.3124 (ptmt)
REVERT: B    6 ASP cc_start: 0.6587 (OUTLIER) cc_final: 0.6045 (p0)
REVERT: B   80 ILE cc_start: 0.2846 (OUTLIER) cc_final: 0.2450 (tp)
REVERT: B   85 ARG cc_start: 0.0817 (ttp-170) cc_final: -0.0586 (ttp-170)
REVERT: B  168 MET cc_start: 0.2830 (OUTLIER) cc_final: 0.2241 (mpp)
REVERT: B  212 PHE cc_start: 0.2490 (OUTLIER) cc_final: 0.1765 (t80)
REVERT: B  239 MET cc_start: 0.3876 (mmp) cc_final: 0.2261 (mtt)
REVERT: B  286 TYR cc_start: -0.1788 (OUTLIER) cc_final: -0.2115 (t80)
REVERT: B  360 MET cc_start: 0.1508 (tpt) cc_final: 0.0168 (mtt)
  outliers start: 43
  outliers final: 26
  residues processed: 87
  average time/residue: 0.1509
  time to fit residues: 18.7846
Evaluate side-chains
  85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 50
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 LYS
Chi-restraints excluded: chain B residue    6 ASP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  366 TYR
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  421 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5279 r_free = 0.5279 target = 0.336830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.5224 r_free = 0.5224 target = 0.330294 restraints weight = 41219.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5238 r_free = 0.5238 target = 0.332099 restraints weight = 28674.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5248 r_free = 0.5248 target = 0.333440 restraints weight = 16621.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5253 r_free = 0.5253 target = 0.333961 restraints weight = 10466.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5261 r_free = 0.5261 target = 0.334926 restraints weight = 8057.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.5265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2559
moved from start:          0.6639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   6750  Z= 0.212
  Angle     :  0.713   6.867   9128  Z= 0.394
  Chirality :  0.045   0.166   1026
  Planarity :  0.005   0.057   1198
  Dihedral  :  7.735  51.779    950
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 19.11
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 15.09 %
    Favored  : 84.68 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 21.55 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -4.02 (0.25), residues: 868
  helix: -1.63 (0.29), residues: 257
  sheet: -2.99 (0.55), residues: 77
  loop : -3.35 (0.23), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 313 
 TYR   0.016   0.002   TYR A 278 
 PHE   0.019   0.002   PHE B 165 
 TRP   0.006   0.002   TRP A 303 
 HIS   0.006   0.002   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 6750)
  covalent geometry    : angle       0.71349 ( 9128)
  hydrogen bonds       : bond        0.03950 (  206)
  hydrogen bonds       : angle       6.68928 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 50
  time to evaluate  : 0.340 
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: A   82 TYR cc_start: 0.3117 (OUTLIER) cc_final: 0.1933 (t80)
REVERT: A  235 GLU cc_start: 0.1244 (OUTLIER) cc_final: -0.2240 (mt-10)
REVERT: A  259 TYR cc_start: 0.0310 (OUTLIER) cc_final: -0.0413 (t80)
REVERT: A  435 LYS cc_start: 0.3350 (OUTLIER) cc_final: 0.2908 (ptmt)
REVERT: B   80 ILE cc_start: 0.3823 (OUTLIER) cc_final: 0.2935 (tp)
REVERT: B   85 ARG cc_start: 0.0879 (ttp-170) cc_final: 0.0074 (ttm170)
REVERT: B  212 PHE cc_start: 0.2602 (OUTLIER) cc_final: 0.1858 (t80)
REVERT: B  239 MET cc_start: 0.3353 (mmp) cc_final: 0.2260 (mmm)
REVERT: B  286 TYR cc_start: -0.1308 (OUTLIER) cc_final: -0.1827 (t80)
REVERT: B  360 MET cc_start: 0.1601 (tpt) cc_final: 0.0111 (mtt)
  outliers start: 37
  outliers final: 27
  residues processed: 80
  average time/residue: 0.1545
  time to fit residues: 17.5532
Evaluate side-chains
  83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 49
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain A residue  435 LYS
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  366 TYR
Chi-restraints excluded: chain B residue  421 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
B  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5302 r_free = 0.5302 target = 0.339826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.5241 r_free = 0.5241 target = 0.332790 restraints weight = 41906.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5255 r_free = 0.5255 target = 0.334587 restraints weight = 24978.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5270 r_free = 0.5270 target = 0.336129 restraints weight = 16455.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.5279 r_free = 0.5279 target = 0.337115 restraints weight = 11040.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.5285 r_free = 0.5285 target = 0.337854 restraints weight = 7596.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.5288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2403
moved from start:          0.6492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6750  Z= 0.119
  Angle     :  0.585   4.664   9128  Z= 0.321
  Chirality :  0.042   0.149   1026
  Planarity :  0.004   0.036   1198
  Dihedral  :  6.877  54.303    950
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.90 %
    Favored  : 86.87 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 23.02 %
    Favored  : 73.02 %
  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: -3.61 (0.26), residues: 868
  helix: -1.06 (0.30), residues: 258
  sheet: -2.57 (0.51), residues: 98
  loop : -3.25 (0.24), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.014   0.001   TYR A 278 
 PHE   0.014   0.001   PHE B 242 
 TRP   0.008   0.001   TRP B 303 
 HIS   0.005   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6750)
  covalent geometry    : angle       0.58531 ( 9128)
  hydrogen bonds       : bond        0.03361 (  206)
  hydrogen bonds       : angle       5.99799 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 53
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TYR cc_start: 0.2698 (OUTLIER) cc_final: 0.1704 (t80)
REVERT: A  259 TYR cc_start: 0.0245 (OUTLIER) cc_final: -0.0376 (t80)
REVERT: A  376 GLU cc_start: 0.0696 (mm-30) cc_final: -0.0217 (mt-10)
REVERT: B   85 ARG cc_start: 0.1562 (ttp-170) cc_final: 0.0510 (ttp-170)
REVERT: B  170 VAL cc_start: 0.4987 (OUTLIER) cc_final: 0.4463 (t)
REVERT: B  212 PHE cc_start: 0.2562 (OUTLIER) cc_final: 0.1780 (t80)
REVERT: B  239 MET cc_start: 0.3126 (mmp) cc_final: 0.2079 (mmt)
REVERT: B  286 TYR cc_start: -0.1606 (OUTLIER) cc_final: -0.2125 (t80)
REVERT: B  360 MET cc_start: 0.1602 (tpt) cc_final: 0.0312 (mtt)
  outliers start: 27
  outliers final: 18
  residues processed: 73
  average time/residue: 0.1543
  time to fit residues: 15.7808
Evaluate side-chains
  74 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.339965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.5242 r_free = 0.5242 target = 0.333005 restraints weight = 41760.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.334909 restraints weight = 25668.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.5271 r_free = 0.5271 target = 0.336315 restraints weight = 16333.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.5280 r_free = 0.5280 target = 0.337283 restraints weight = 11072.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.338016 restraints weight = 7668.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.5289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2396
moved from start:          0.6552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6750  Z= 0.119
  Angle     :  0.573   4.356   9128  Z= 0.312
  Chirality :  0.041   0.143   1026
  Planarity :  0.004   0.033   1198
  Dihedral  :  6.590  56.205    950
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.79 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 23.90 %
    Favored  : 73.17 %
  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: -3.40 (0.26), residues: 868
  helix: -0.85 (0.30), residues: 265
  sheet: -2.46 (0.53), residues: 93
  loop : -3.16 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.014   0.001   TYR A 278 
 PHE   0.016   0.001   PHE B 242 
 TRP   0.007   0.001   TRP B 303 
 HIS   0.004   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6750)
  covalent geometry    : angle       0.57298 ( 9128)
  hydrogen bonds       : bond        0.03144 (  206)
  hydrogen bonds       : angle       5.79946 (  555)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 TYR cc_start: 0.0313 (OUTLIER) cc_final: -0.0195 (t80)
REVERT: A  376 GLU cc_start: 0.0654 (mm-30) cc_final: -0.0172 (mt-10)
REVERT: B   80 ILE cc_start: 0.3587 (OUTLIER) cc_final: 0.3276 (mm)
REVERT: B   85 ARG cc_start: 0.1410 (ttp-170) cc_final: 0.0345 (ttm170)
REVERT: B  212 PHE cc_start: 0.2538 (OUTLIER) cc_final: 0.1759 (t80)
REVERT: B  239 MET cc_start: 0.3115 (mmp) cc_final: 0.1817 (mmm)
REVERT: B  360 MET cc_start: 0.1923 (tpt) cc_final: 0.0485 (mtt)
  outliers start: 20
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1604
  time to fit residues: 16.0284
Evaluate side-chains
  70 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  259 TYR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  423 GLN
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  212 PHE
Chi-restraints excluded: chain B residue  242 PHE
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 82 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 78 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN
B 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5269 r_free = 0.5269 target = 0.335519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5214 r_free = 0.5214 target = 0.328988 restraints weight = 41194.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5226 r_free = 0.5226 target = 0.330564 restraints weight = 29586.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5238 r_free = 0.5238 target = 0.332021 restraints weight = 16344.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5239 r_free = 0.5239 target = 0.332160 restraints weight = 11228.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.5249 r_free = 0.5249 target = 0.333274 restraints weight = 9071.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.5252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2657
moved from start:          0.7273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.108   6750  Z= 0.297
  Angle     :  0.853   8.156   9128  Z= 0.471
  Chirality :  0.050   0.253   1026
  Planarity :  0.007   0.089   1198
  Dihedral  :  8.080  59.104    950
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 23.89
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 16.59 %
    Favored  : 83.06 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 23.31 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.96 (0.25), residues: 868
  helix: -1.40 (0.30), residues: 256
  sheet: -2.96 (0.53), residues: 77
  loop : -3.42 (0.23), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 313 
 TYR   0.023   0.003   TYR A 278 
 PHE   0.029   0.003   PHE B 165 
 TRP   0.015   0.003   TRP A 181 
 HIS   0.006   0.002   HIS A   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 ( 6750)
  covalent geometry    : angle       0.85341 ( 9128)
  hydrogen bonds       : bond        0.04471 (  206)
  hydrogen bonds       : angle       6.86538 (  555)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2018.07 seconds
wall clock time: 35 minutes 6.30 seconds (2106.30 seconds total)