Starting phenix.real_space_refine
on Tue Mar  3 15:35:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rp6_24613/03_2026/7rp6_24613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rp6_24613/03_2026/7rp6_24613.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rp6_24613/03_2026/7rp6_24613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rp6_24613/03_2026/7rp6_24613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rp6_24613/03_2026/7rp6_24613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rp6_24613/03_2026/7rp6_24613.cif"
  }
  resolution = 3.78
  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=   0.003 sd=   0.036
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: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4435      2.51       5
     N    1138      2.21       5
     O    1140      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6753
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3374
          Classifications: {'peptide': 450}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 430}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 3379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3379
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 19, 'TRANS': 430}
  Time building chain proxies: 1.48, per 1000 atoms: 0.22
  Number of scatterers: 6753
  At special positions: 0
  Unit cell: (77.552, 76.504, 114.232, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1140      8.00
     N    1138      7.00
     C    4435      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 302 " - pdb=" SG  CYS B 347 " distance=2.78

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 259.8 milliseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      77.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 27
      removed outlier: 3.696A  pdb=" N   ARG A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 71
      removed outlier: 4.253A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A  41 " --> pdb=" O   PHE A  37 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A  42 " --> pdb=" O   MET A  38 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   LEU A  68 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   VAL A  69 " --> pdb=" O   MET A  65 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   HIS A  70 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   THR A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 100
      removed outlier: 4.116A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLY A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.839A  pdb=" N   GLY A 105 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.714A  pdb=" N   ALA A 115 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 135
      removed outlier: 3.788A  pdb=" N   LEU A 128 " --> pdb=" O   TRP A 124 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
      removed outlier: 5.373A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 148 through 165
      removed outlier: 3.593A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP A 164 " --> pdb=" O   ARG A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 188
      removed outlier: 4.256A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 214 through 231
      removed outlier: 3.635A  pdb=" N   VAL A 218 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY A 221 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE A 223 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 283
      removed outlier: 3.948A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.704A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 308
      removed outlier: 3.851A  pdb=" N   CYS A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   LEU A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 324
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 4.194A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 379
      removed outlier: 3.705A  pdb=" N   LEU A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
    Processing helix  chain 'A' and resid 385 through 395
      removed outlier: 4.442A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
    Processing helix  chain 'A' and resid 406 through 415
      removed outlier: 4.240A  pdb=" N   VAL A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.786A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 4.055A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU A 459 " --> pdb=" O   LYS A 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 26
      removed outlier: 3.776A  pdb=" N   ARG B  18 " --> pdb=" O   ALA B  14 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG B  19 " --> pdb=" O   ARG B  15 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 67
      removed outlier: 4.526A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL B  41 " --> pdb=" O   PHE B  37 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B  42 " --> pdb=" O   MET B  38 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 70
      No H-bonds generated for 'chain 'B' and resid 68 through 70'
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 4.069A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ALA B  82 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA B  90 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLY B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA B 101 " --> pdb=" O   VAL B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 105
      removed outlier: 3.538A  pdb=" N   GLY B 105 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 102 through 105'
    Processing helix  chain 'B' and resid 108 through 116
    Processing helix  chain 'B' and resid 123 through 141
      removed outlier: 3.755A  pdb=" N   LEU B 128 " --> pdb=" O   TRP B 124 " (cutoff:3.500A)
      Proline residue:  B 129  - end of helix
      removed outlier: 5.025A  pdb=" N   PHE B 133 " --> pdb=" O   PRO B 129 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU B 136 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 165
      removed outlier: 3.651A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 188
      removed outlier: 4.266A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA B 182 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 214 through 232
      removed outlier: 4.098A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 250
      No H-bonds generated for 'chain 'B' and resid 248 through 250'
    Processing helix  chain 'B' and resid 251 through 283
      removed outlier: 3.876A  pdb=" N   TYR B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.887A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 308
      removed outlier: 3.582A  pdb=" N   CYS B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 313
      removed outlier: 3.643A  pdb=" N   THR B 312 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER B 313 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 309 through 313'
    Processing helix  chain 'B' and resid 319 through 324
      removed outlier: 3.587A  pdb=" N   ALA B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 348
      removed outlier: 3.939A  pdb=" N   PHE B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 351
      No H-bonds generated for 'chain 'B' and resid 349 through 351'
    Processing helix  chain 'B' and resid 357 through 379
      removed outlier: 4.062A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
    Processing helix  chain 'B' and resid 386 through 395
      removed outlier: 4.166A  pdb=" N   ALA B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE B 391 " --> pdb=" O   GLY B 387 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 402
    Processing helix  chain 'B' and resid 406 through 415
      removed outlier: 4.029A  pdb=" N   VAL B 412 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 438
      removed outlier: 3.597A  pdb=" N   THR B 428 " --> pdb=" O   PRO B 424 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   THR B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ALA B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 459
      removed outlier: 4.136A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU B 459 " --> pdb=" O   LYS B 455 " (cutoff:3.500A)

    415 hydrogen bonds defined for protein.
    1236 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: 0.84

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2131
        1.34 -     1.46: 1433
        1.46 -     1.58: 3258
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 6896
  Sorted by residual:
  bond pdb=" N   CYS B 302 "
       pdb=" CA  CYS B 302 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.027 1.25e-02 6.40e+03 4.53e+00
  bond pdb=" N   LEU B 301 "
       pdb=" CA  LEU B 301 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.20e-02 6.94e+03 3.60e+00
  bond pdb=" C   LEU B 128 "
       pdb=" N   PRO B 129 "
    ideal  model  delta    sigma   weight residual
    1.334  1.377 -0.043 2.34e-02 1.83e+03 3.38e+00
  bond pdb=" N   ASN B 233 "
       pdb=" CA  ASN B 233 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.026 1.42e-02 4.96e+03 3.38e+00
  bond pdb=" C   LEU A 128 "
       pdb=" N   PRO A 129 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.043 2.34e-02 1.83e+03 3.31e+00
  ... (remaining 6891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 9061
        2.40 -     4.80: 246
        4.80 -     7.20: 35
        7.20 -     9.59: 14
        9.59 -    11.99: 2
  Bond angle restraints: 9358
  Sorted by residual:
  angle pdb=" C   PHE A 232 "
        pdb=" N   ASN A 233 "
        pdb=" CA  ASN A 233 "
      ideal   model   delta    sigma   weight residual
     122.77  115.61    7.16 1.33e+00 5.65e-01 2.90e+01
  angle pdb=" CA  ILE B 320 "
        pdb=" C   ILE B 320 "
        pdb=" N   PRO B 321 "
      ideal   model   delta    sigma   weight residual
     120.83  124.06   -3.23 6.10e-01 2.69e+00 2.80e+01
  angle pdb=" N   LEU B 301 "
        pdb=" CA  LEU B 301 "
        pdb=" C   LEU B 301 "
      ideal   model   delta    sigma   weight residual
     111.14  106.08    5.06 1.08e+00 8.57e-01 2.19e+01
  angle pdb=" C   PHE B 166 "
        pdb=" N   ARG B 167 "
        pdb=" CA  ARG B 167 "
      ideal   model   delta    sigma   weight residual
     121.54  130.05   -8.51 1.91e+00 2.74e-01 1.99e+01
  angle pdb=" C   ASN B 233 "
        pdb=" N   HIS B 234 "
        pdb=" CA  HIS B 234 "
      ideal   model   delta    sigma   weight residual
     121.19  127.74   -6.55 1.59e+00 3.96e-01 1.70e+01
  ... (remaining 9353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 3503
       17.08 -    34.16: 409
       34.16 -    51.23: 84
       51.23 -    68.31: 9
       68.31 -    85.39: 8
  Dihedral angle restraints: 4013
    sinusoidal: 1525
      harmonic: 2488
  Sorted by residual:
  dihedral pdb=" CB  CYS B 302 "
           pdb=" SG  CYS B 302 "
           pdb=" SG  CYS B 347 "
           pdb=" CB  CYS B 347 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.18  -84.18     1      1.00e+01 1.00e-02 8.63e+01
  dihedral pdb=" CA  VAL B 162 "
           pdb=" C   VAL B 162 "
           pdb=" N   LEU B 163 "
           pdb=" CA  LEU B 163 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.06   29.94     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  VAL A 162 "
           pdb=" C   VAL A 162 "
           pdb=" N   LEU A 163 "
           pdb=" CA  LEU A 163 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.48   28.52     0      5.00e+00 4.00e-02 3.25e+01
  ... (remaining 4010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 957
       0.079 -    0.159: 133
       0.159 -    0.238: 8
       0.238 -    0.318: 3
       0.318 -    0.397: 1
  Chirality restraints: 1102
  Sorted by residual:
  chirality pdb=" CB  ILE B 356 "
            pdb=" CA  ILE B 356 "
            pdb=" CG1 ILE B 356 "
            pdb=" CG2 ILE B 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CB  ILE B 320 "
            pdb=" CA  ILE B 320 "
            pdb=" CG1 ILE B 320 "
            pdb=" CG2 ILE B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 1099 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 300 "    0.023 2.00e-02 2.50e+03   4.58e-02 2.10e+01
        pdb=" C   GLY B 300 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   GLY B 300 "    0.030 2.00e-02 2.50e+03
        pdb=" N   LEU B 301 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 205 "    0.048 5.00e-02 4.00e+02   7.23e-02 8.37e+00
        pdb=" N   PRO A 206 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "   -0.042 5.00e-02 4.00e+02   6.34e-02 6.43e+00
        pdb=" N   PRO A 150 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2284
        2.85 -     3.36: 6543
        3.36 -     3.87: 11297
        3.87 -     4.39: 12540
        4.39 -     4.90: 21838
  Nonbonded interactions: 54502
  Sorted by model distance:
  nonbonded pdb=" O   SER B 350 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OD1 ASN B 287 "
            pdb=" OG1 THR B 289 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" NZ  LYS B 131 "
            pdb=" OE1 GLN B 153 "
     model   vdw
     2.378 3.120
  nonbonded pdb=" NZ  LYS A 131 "
            pdb=" OE1 GLN A 153 "
     model   vdw
     2.379 3.120
  nonbonded pdb=" OD1 ASP A 278 "
            pdb=" NH1 ARG A 451 "
     model   vdw
     2.396 3.120
  ... (remaining 54497 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 12 through 233 or (resid 234 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 235 through 461))
}

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:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.340
  Find NCS groups from input model:        0.080
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
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      :  0.011   0.753   6897  Z= 0.518
  Angle     :  1.129  51.483   9360  Z= 0.590
  Chirality :  0.058   0.397   1102
  Planarity :  0.008   0.072   1175
  Dihedral  : 14.846  85.390   2438
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.60 %
    Favored  : 89.81 %
  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 are not related in a simple way.
  whole: -4.72 (0.21), residues: 896
  helix: -2.99 (0.14), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.79 (0.36), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 403 
 TYR   0.012   0.002   TYR B 229 
 PHE   0.028   0.002   PHE A 219 
 TRP   0.007   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 6896)
  covalent geometry    : angle       0.95603 ( 9358)
  SS BOND              : bond        0.75256 (    1)
  SS BOND              : angle      41.04439 (    2)
  hydrogen bonds       : bond        0.07430 (  415)
  hydrogen bonds       : angle       4.98970 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 192
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8375 (t80) cc_final: 0.7952 (t80)
REVERT: A  132 PHE cc_start: 0.8059 (t80) cc_final: 0.7834 (t80)
REVERT: A  210 TYR cc_start: 0.8289 (t80) cc_final: 0.7947 (t80)
REVERT: A  228 MET cc_start: 0.8354 (tpp) cc_final: 0.7833 (mmt)
REVERT: A  253 TRP cc_start: 0.8076 (p-90) cc_final: 0.7599 (p-90)
REVERT: A  318 ASN cc_start: 0.7608 (p0) cc_final: 0.7392 (p0)
REVERT: A  459 GLU cc_start: 0.7254 (mp0) cc_final: 0.6794 (mp0)
REVERT: B   16 LEU cc_start: 0.8706 (pp) cc_final: 0.8418 (pp)
REVERT: B  100 TYR cc_start: 0.8152 (m-80) cc_final: 0.7716 (m-80)
REVERT: B  228 MET cc_start: 0.7671 (mmm) cc_final: 0.7311 (mmm)
REVERT: B  264 ILE cc_start: 0.8808 (tt) cc_final: 0.8582 (tt)
REVERT: B  335 PHE cc_start: 0.8690 (t80) cc_final: 0.8418 (t80)
REVERT: B  342 ILE cc_start: 0.8844 (mm) cc_final: 0.8626 (tp)
REVERT: B  421 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7956 (pp)
  outliers start: 4
  outliers final: 1
  residues processed: 194
  average time/residue: 0.0665
  time to fit residues: 17.8243
Evaluate side-chains
  145 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0670
   chunk 74 optimal weight:    8.9990
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A  70 HIS
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
B  70 HIS
B 270 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.139317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.111364 restraints weight = 9753.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.114673 restraints weight = 5939.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.116940 restraints weight = 4316.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118388 restraints weight = 3510.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.118666 restraints weight = 3099.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6897  Z= 0.150
  Angle     :  0.648   9.223   9360  Z= 0.322
  Chirality :  0.042   0.161   1102
  Planarity :  0.005   0.058   1175
  Dihedral  :  5.422  29.515    964
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.81 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.26), residues: 896
  helix: -1.48 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.36 (0.38), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.023   0.002   PHE B  92 
 TRP   0.018   0.001   TRP A 291 
 HIS   0.006   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6896)
  covalent geometry    : angle       0.64459 ( 9358)
  SS BOND              : bond        0.01723 (    1)
  SS BOND              : angle       4.66614 (    2)
  hydrogen bonds       : bond        0.03284 (  415)
  hydrogen bonds       : angle       4.10888 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8412 (t80) cc_final: 0.8075 (t80)
REVERT: A  132 PHE cc_start: 0.8194 (t80) cc_final: 0.7890 (t80)
REVERT: A  210 TYR cc_start: 0.8352 (t80) cc_final: 0.7942 (t80)
REVERT: A  228 MET cc_start: 0.8594 (tpp) cc_final: 0.7967 (mmt)
REVERT: A  253 TRP cc_start: 0.8208 (p-90) cc_final: 0.7646 (p-90)
REVERT: A  421 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8051 (pp)
REVERT: A  459 GLU cc_start: 0.7483 (mp0) cc_final: 0.6959 (mp0)
REVERT: B   91 MET cc_start: 0.8241 (mtm) cc_final: 0.7887 (mtm)
REVERT: B  100 TYR cc_start: 0.8327 (m-80) cc_final: 0.7881 (m-80)
REVERT: B  228 MET cc_start: 0.7849 (mmm) cc_final: 0.7375 (mmm)
REVERT: B  264 ILE cc_start: 0.8666 (tt) cc_final: 0.8430 (tt)
REVERT: B  284 HIS cc_start: 0.8251 (p-80) cc_final: 0.7949 (p90)
REVERT: B  335 PHE cc_start: 0.8722 (t80) cc_final: 0.8489 (t80)
REVERT: B  421 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7703 (pp)
  outliers start: 25
  outliers final: 15
  residues processed: 177
  average time/residue: 0.0562
  time to fit residues: 14.4524
Evaluate side-chains
  163 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
A 437 GLN
B  63 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.136969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.109099 restraints weight = 9626.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.112239 restraints weight = 5866.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.114359 restraints weight = 4314.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.115877 restraints weight = 3546.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.116577 restraints weight = 3118.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6897  Z= 0.135
  Angle     :  0.615   9.223   9360  Z= 0.305
  Chirality :  0.042   0.161   1102
  Planarity :  0.005   0.052   1175
  Dihedral  :  5.035  29.203    962
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 20.09 %
    Favored  : 75.33 %
  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 are not related in a simple way.
  whole: -1.77 (0.28), residues: 896
  helix: -0.75 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.03 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  98 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.012   0.001   PHE A 219 
 TRP   0.020   0.002   TRP B 291 
 HIS   0.005   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6896)
  covalent geometry    : angle       0.61405 ( 9358)
  SS BOND              : bond        0.00888 (    1)
  SS BOND              : angle       2.83589 (    2)
  hydrogen bonds       : bond        0.03135 (  415)
  hydrogen bonds       : angle       3.94030 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8449 (t80) cc_final: 0.8140 (t80)
REVERT: A  132 PHE cc_start: 0.8199 (t80) cc_final: 0.7898 (t80)
REVERT: A  210 TYR cc_start: 0.8351 (t80) cc_final: 0.7962 (t80)
REVERT: A  253 TRP cc_start: 0.8224 (p-90) cc_final: 0.7633 (p-90)
REVERT: A  421 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8132 (pp)
REVERT: A  459 GLU cc_start: 0.7547 (mp0) cc_final: 0.7062 (mp0)
REVERT: B   91 MET cc_start: 0.8260 (mtm) cc_final: 0.7945 (mtm)
REVERT: B  100 TYR cc_start: 0.8344 (m-80) cc_final: 0.7820 (m-80)
REVERT: B  228 MET cc_start: 0.7878 (mmm) cc_final: 0.7497 (mmm)
REVERT: B  264 ILE cc_start: 0.8734 (tt) cc_final: 0.8510 (tt)
REVERT: B  335 PHE cc_start: 0.8731 (t80) cc_final: 0.8464 (t80)
REVERT: B  421 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7760 (pp)
  outliers start: 31
  outliers final: 18
  residues processed: 170
  average time/residue: 0.0556
  time to fit residues: 14.0338
Evaluate side-chains
  165 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   98 ARG
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0070
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
A  74 ASN
B  63 GLN
B  74 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.139367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.111760 restraints weight = 9705.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.115048 restraints weight = 5942.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.117230 restraints weight = 4338.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.118547 restraints weight = 3549.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.119468 restraints weight = 3136.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6897  Z= 0.123
  Angle     :  0.602   9.397   9360  Z= 0.298
  Chirality :  0.042   0.137   1102
  Planarity :  0.005   0.048   1175
  Dihedral  :  4.869  29.097    962
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 20.97 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.29), residues: 896
  helix: -0.33 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.72 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  18 
 TYR   0.009   0.001   TYR B 100 
 PHE   0.023   0.001   PHE B  92 
 TRP   0.018   0.002   TRP A  59 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6896)
  covalent geometry    : angle       0.60184 ( 9358)
  SS BOND              : bond        0.00690 (    1)
  SS BOND              : angle       2.01713 (    2)
  hydrogen bonds       : bond        0.03042 (  415)
  hydrogen bonds       : angle       3.84844 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 155
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   92 PHE cc_start: 0.8421 (t80) cc_final: 0.8112 (t80)
REVERT: A  210 TYR cc_start: 0.8342 (t80) cc_final: 0.7980 (t80)
REVERT: A  228 MET cc_start: 0.8438 (mmm) cc_final: 0.7958 (mmt)
REVERT: A  253 TRP cc_start: 0.8237 (p-90) cc_final: 0.7653 (p-90)
REVERT: A  421 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8133 (pp)
REVERT: A  438 PHE cc_start: 0.7614 (m-10) cc_final: 0.6863 (t80)
REVERT: A  459 GLU cc_start: 0.7604 (mp0) cc_final: 0.7172 (mp0)
REVERT: B   20 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: B   91 MET cc_start: 0.8254 (mtm) cc_final: 0.7938 (mtm)
REVERT: B  100 TYR cc_start: 0.8269 (m-80) cc_final: 0.7741 (m-80)
REVERT: B  264 ILE cc_start: 0.8723 (tt) cc_final: 0.8492 (tt)
REVERT: B  335 PHE cc_start: 0.8686 (t80) cc_final: 0.8399 (t80)
REVERT: B  421 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7713 (pp)
  outliers start: 33
  outliers final: 19
  residues processed: 173
  average time/residue: 0.0493
  time to fit residues: 12.9101
Evaluate side-chains
  170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0980
   chunk 89 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0570
   chunk 67 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.4900

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
B  63 GLN
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.141071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.113440 restraints weight = 9663.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.116755 restraints weight = 5886.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.118769 restraints weight = 4289.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.120346 restraints weight = 3535.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.120993 restraints weight = 3095.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6897  Z= 0.118
  Angle     :  0.612   9.989   9360  Z= 0.304
  Chirality :  0.042   0.165   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.798  29.185    962
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 22.45 %
    Favored  : 73.26 %
  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 are not related in a simple way.
  whole: -0.94 (0.29), residues: 896
  helix: -0.18 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.64 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  98 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.009   0.001   PHE A 348 
 TRP   0.024   0.001   TRP A  59 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6896)
  covalent geometry    : angle       0.61182 ( 9358)
  SS BOND              : bond        0.00628 (    1)
  SS BOND              : angle       1.71320 (    2)
  hydrogen bonds       : bond        0.03026 (  415)
  hydrogen bonds       : angle       3.89017 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8298 (t80) cc_final: 0.7990 (t80)
REVERT: A  210 TYR cc_start: 0.8337 (t80) cc_final: 0.7988 (t80)
REVERT: A  228 MET cc_start: 0.8399 (mmm) cc_final: 0.7919 (mmt)
REVERT: A  253 TRP cc_start: 0.8221 (p-90) cc_final: 0.7681 (p-90)
REVERT: A  421 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8192 (pp)
REVERT: A  438 PHE cc_start: 0.7632 (m-10) cc_final: 0.6902 (t80)
REVERT: A  459 GLU cc_start: 0.7548 (mp0) cc_final: 0.7113 (mp0)
REVERT: B   20 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: B  100 TYR cc_start: 0.8240 (m-80) cc_final: 0.7745 (m-80)
REVERT: B  228 MET cc_start: 0.7806 (mmm) cc_final: 0.7476 (mmm)
REVERT: B  264 ILE cc_start: 0.8723 (tt) cc_final: 0.8503 (tt)
REVERT: B  335 PHE cc_start: 0.8669 (t80) cc_final: 0.8385 (t80)
REVERT: B  421 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7732 (pp)
  outliers start: 29
  outliers final: 16
  residues processed: 165
  average time/residue: 0.0452
  time to fit residues: 11.5154
Evaluate side-chains
  163 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
B  63 GLN
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.136795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.108949 restraints weight = 9845.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.112105 restraints weight = 6065.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.114101 restraints weight = 4469.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.115689 restraints weight = 3691.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.116460 restraints weight = 3241.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6897  Z= 0.185
  Angle     :  0.650  10.275   9360  Z= 0.322
  Chirality :  0.044   0.152   1102
  Planarity :  0.005   0.047   1175
  Dihedral  :  4.871  27.886    962
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.93 %
    Favored  : 71.34 %
  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 are not related in a simple way.
  whole: -0.85 (0.29), residues: 896
  helix: -0.14 (0.21), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.51 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  98 
 TYR   0.009   0.001   TYR B 100 
 PHE   0.025   0.002   PHE B  92 
 TRP   0.020   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 6896)
  covalent geometry    : angle       0.64969 ( 9358)
  SS BOND              : bond        0.00469 (    1)
  SS BOND              : angle       1.70839 (    2)
  hydrogen bonds       : bond        0.03227 (  415)
  hydrogen bonds       : angle       3.96082 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8497 (t80) cc_final: 0.8245 (t80)
REVERT: A  210 TYR cc_start: 0.8407 (t80) cc_final: 0.8070 (t80)
REVERT: A  253 TRP cc_start: 0.8372 (p-90) cc_final: 0.7783 (p-90)
REVERT: A  421 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8119 (pp)
REVERT: A  438 PHE cc_start: 0.7707 (m-10) cc_final: 0.6932 (t80)
REVERT: A  459 GLU cc_start: 0.7602 (mp0) cc_final: 0.7254 (mp0)
REVERT: B   20 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7761 (tm-30)
REVERT: B   62 ASN cc_start: 0.8634 (t0) cc_final: 0.8412 (t0)
REVERT: B   63 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8388 (mp-120)
REVERT: B  100 TYR cc_start: 0.8339 (m-80) cc_final: 0.7848 (m-80)
REVERT: B  228 MET cc_start: 0.7987 (mmm) cc_final: 0.7662 (mmm)
REVERT: B  264 ILE cc_start: 0.8771 (tt) cc_final: 0.8545 (tt)
REVERT: B  335 PHE cc_start: 0.8714 (t80) cc_final: 0.8424 (t80)
REVERT: B  421 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7852 (pp)
  outliers start: 32
  outliers final: 26
  residues processed: 167
  average time/residue: 0.0523
  time to fit residues: 13.0479
Evaluate side-chains
  173 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.137612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.109811 restraints weight = 9637.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.113023 restraints weight = 5882.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.115100 restraints weight = 4314.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.115806 restraints weight = 3555.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.117172 restraints weight = 3255.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6897  Z= 0.139
  Angle     :  0.621  10.498   9360  Z= 0.307
  Chirality :  0.042   0.144   1102
  Planarity :  0.004   0.045   1175
  Dihedral  :  4.796  29.369    962
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 24.08 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.29), residues: 896
  helix:  0.04 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.59 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  98 
 TYR   0.010   0.001   TYR B 419 
 PHE   0.011   0.001   PHE A 348 
 TRP   0.020   0.002   TRP A 291 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6896)
  covalent geometry    : angle       0.62061 ( 9358)
  SS BOND              : bond        0.00567 (    1)
  SS BOND              : angle       1.67890 (    2)
  hydrogen bonds       : bond        0.03073 (  415)
  hydrogen bonds       : angle       3.90906 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8398 (t80) cc_final: 0.8090 (t80)
REVERT: A  210 TYR cc_start: 0.8420 (t80) cc_final: 0.8079 (t80)
REVERT: A  253 TRP cc_start: 0.8346 (p-90) cc_final: 0.7755 (p-90)
REVERT: A  421 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8133 (pp)
REVERT: A  438 PHE cc_start: 0.7596 (m-10) cc_final: 0.6811 (t80)
REVERT: A  459 GLU cc_start: 0.7597 (mp0) cc_final: 0.7221 (mp0)
REVERT: B   20 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: B  100 TYR cc_start: 0.8339 (m-80) cc_final: 0.7818 (m-80)
REVERT: B  128 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8330 (tt)
REVERT: B  228 MET cc_start: 0.7960 (mmm) cc_final: 0.7626 (mmm)
REVERT: B  264 ILE cc_start: 0.8746 (tt) cc_final: 0.8529 (tt)
REVERT: B  335 PHE cc_start: 0.8700 (t80) cc_final: 0.8389 (t80)
REVERT: B  421 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7817 (pp)
  outliers start: 30
  outliers final: 19
  residues processed: 157
  average time/residue: 0.0474
  time to fit residues: 11.3695
Evaluate side-chains
  162 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  291 TRP
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 9 optimal weight:    0.2980
   chunk 48 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0370
   chunk 36 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.5860

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.140374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.112703 restraints weight = 9704.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.116007 restraints weight = 5887.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.118186 restraints weight = 4295.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.119527 restraints weight = 3530.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.120516 restraints weight = 3110.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6897  Z= 0.121
  Angle     :  0.611  10.637   9360  Z= 0.302
  Chirality :  0.042   0.154   1102
  Planarity :  0.004   0.045   1175
  Dihedral  :  4.694  29.233    962
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.82 %
    Favored  : 71.20 %
  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 are not related in a simple way.
  whole: -0.44 (0.29), residues: 896
  helix:  0.21 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.55 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  98 
 TYR   0.009   0.001   TYR B 419 
 PHE   0.028   0.001   PHE B  92 
 TRP   0.020   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6896)
  covalent geometry    : angle       0.61072 ( 9358)
  SS BOND              : bond        0.00562 (    1)
  SS BOND              : angle       1.52524 (    2)
  hydrogen bonds       : bond        0.03011 (  415)
  hydrogen bonds       : angle       3.86816 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8295 (t80) cc_final: 0.7985 (t80)
REVERT: A  210 TYR cc_start: 0.8399 (t80) cc_final: 0.8074 (t80)
REVERT: A  253 TRP cc_start: 0.8322 (p-90) cc_final: 0.7692 (p-90)
REVERT: A  421 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8212 (pp)
REVERT: A  438 PHE cc_start: 0.7483 (m-10) cc_final: 0.6763 (t80)
REVERT: A  459 GLU cc_start: 0.7579 (mp0) cc_final: 0.7218 (mp0)
REVERT: B   20 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7675 (tm-30)
REVERT: B  100 TYR cc_start: 0.8269 (m-80) cc_final: 0.7769 (m-80)
REVERT: B  128 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8334 (tt)
REVERT: B  228 MET cc_start: 0.7849 (mmm) cc_final: 0.7525 (mmm)
REVERT: B  264 ILE cc_start: 0.8743 (tt) cc_final: 0.8530 (tt)
REVERT: B  329 SER cc_start: 0.8944 (t) cc_final: 0.8743 (m)
REVERT: B  335 PHE cc_start: 0.8697 (t80) cc_final: 0.8354 (t80)
REVERT: B  419 TYR cc_start: 0.7314 (t80) cc_final: 0.6864 (t80)
REVERT: B  421 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7777 (pp)
  outliers start: 27
  outliers final: 21
  residues processed: 165
  average time/residue: 0.0528
  time to fit residues: 13.0481
Evaluate side-chains
  162 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  291 TRP
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0060
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 68 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0570
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.140194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.112857 restraints weight = 9662.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.116111 restraints weight = 5860.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.118280 restraints weight = 4288.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.119340 restraints weight = 3508.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.120489 restraints weight = 3130.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6897  Z= 0.131
  Angle     :  0.626  10.450   9360  Z= 0.311
  Chirality :  0.042   0.146   1102
  Planarity :  0.004   0.045   1175
  Dihedral  :  4.666  28.558    962
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 24.82 %
    Favored  : 70.75 %
  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 are not related in a simple way.
  whole: -0.31 (0.29), residues: 896
  helix:  0.30 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.47 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  98 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.017   0.001   PHE A 166 
 TRP   0.021   0.002   TRP A 291 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6896)
  covalent geometry    : angle       0.62541 ( 9358)
  SS BOND              : bond        0.00545 (    1)
  SS BOND              : angle       1.54342 (    2)
  hydrogen bonds       : bond        0.03006 (  415)
  hydrogen bonds       : angle       3.88942 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8319 (t80) cc_final: 0.8007 (t80)
REVERT: A  210 TYR cc_start: 0.8395 (t80) cc_final: 0.8075 (t80)
REVERT: A  253 TRP cc_start: 0.8341 (p-90) cc_final: 0.7741 (p-90)
REVERT: A  421 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8229 (pp)
REVERT: A  438 PHE cc_start: 0.7467 (m-10) cc_final: 0.6760 (t80)
REVERT: A  459 GLU cc_start: 0.7562 (mp0) cc_final: 0.7216 (mp0)
REVERT: B   20 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7669 (tm-30)
REVERT: B  100 TYR cc_start: 0.8296 (m-80) cc_final: 0.7819 (m-80)
REVERT: B  128 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8341 (tt)
REVERT: B  228 MET cc_start: 0.7872 (mmm) cc_final: 0.7507 (mmm)
REVERT: B  264 ILE cc_start: 0.8776 (tt) cc_final: 0.8569 (tt)
REVERT: B  335 PHE cc_start: 0.8736 (t80) cc_final: 0.8400 (t80)
REVERT: B  421 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7744 (pp)
  outliers start: 30
  outliers final: 22
  residues processed: 157
  average time/residue: 0.0472
  time to fit residues: 11.5081
Evaluate side-chains
  164 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  291 TRP
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 63 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.139941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.112380 restraints weight = 9678.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.115591 restraints weight = 5903.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.117703 restraints weight = 4315.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.119226 restraints weight = 3540.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.120225 restraints weight = 3100.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6897  Z= 0.138
  Angle     :  0.630  10.510   9360  Z= 0.313
  Chirality :  0.042   0.144   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.675  28.702    962
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 25.41 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.29), residues: 896
  helix:  0.36 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.42 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  64 
 TYR   0.007   0.001   TYR B 100 
 PHE   0.031   0.001   PHE B  92 
 TRP   0.022   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6896)
  covalent geometry    : angle       0.62960 ( 9358)
  SS BOND              : bond        0.00588 (    1)
  SS BOND              : angle       1.60828 (    2)
  hydrogen bonds       : bond        0.03026 (  415)
  hydrogen bonds       : angle       3.90382 ( 1236)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8324 (t80) cc_final: 0.8019 (t80)
REVERT: A  210 TYR cc_start: 0.8398 (t80) cc_final: 0.8091 (t80)
REVERT: A  228 MET cc_start: 0.8329 (mmm) cc_final: 0.7873 (mmt)
REVERT: A  253 TRP cc_start: 0.8357 (p-90) cc_final: 0.7751 (p-90)
REVERT: A  421 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8231 (pp)
REVERT: A  438 PHE cc_start: 0.7393 (m-10) cc_final: 0.6719 (t80)
REVERT: A  459 GLU cc_start: 0.7527 (mp0) cc_final: 0.7171 (mp0)
REVERT: B   20 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: B  100 TYR cc_start: 0.8267 (m-80) cc_final: 0.7714 (m-80)
REVERT: B  128 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8341 (tt)
REVERT: B  264 ILE cc_start: 0.8771 (tt) cc_final: 0.8562 (tt)
REVERT: B  335 PHE cc_start: 0.8706 (t80) cc_final: 0.8390 (t80)
REVERT: B  421 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7764 (pp)
  outliers start: 28
  outliers final: 23
  residues processed: 157
  average time/residue: 0.0539
  time to fit residues: 12.7194
Evaluate side-chains
  164 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  291 TRP
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 55 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 74 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.137077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.108504 restraints weight = 9714.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.111735 restraints weight = 5957.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.113947 restraints weight = 4386.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.115292 restraints weight = 3605.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.116351 restraints weight = 3193.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6897  Z= 0.131
  Angle     :  0.633  10.610   9360  Z= 0.315
  Chirality :  0.042   0.140   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.671  28.675    962
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 25.11 %
    Favored  : 70.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.29), residues: 896
  helix:  0.39 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.43 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  98 
 TYR   0.007   0.001   TYR B 100 
 PHE   0.021   0.001   PHE A 166 
 TRP   0.024   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6896)
  covalent geometry    : angle       0.63226 ( 9358)
  SS BOND              : bond        0.00676 (    1)
  SS BOND              : angle       1.63461 (    2)
  hydrogen bonds       : bond        0.03019 (  415)
  hydrogen bonds       : angle       3.90187 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1011.13 seconds
wall clock time: 18 minutes 10.05 seconds (1090.05 seconds total)