Starting phenix.real_space_refine
on Tue Mar 11 20:55:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rp6_24613/03_2025/7rp6_24613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rp6_24613/03_2025/7rp6_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_2025/7rp6_24613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rp6_24613/03_2025/7rp6_24613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rp6_24613/03_2025/7rp6_24613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rp6_24613/03_2025/7rp6_24613.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.84, per 1000 atoms: 0.72
  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: 1.61
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.67
  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: 1.88

  Time building geometry restraints manager: 1.97 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:             0.610
  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:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.680
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.260
-------------------------------------------------------------------------------
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      :  0.006   0.066   6896  Z= 0.373
  Angle     :  0.956  11.992   9358  Z= 0.516
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.007   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 284 
 PHE   0.028   0.002   PHE A 219 
 TYR   0.012   0.002   TYR B 229 
 ARG   0.003   0.000   ARG B 403 

*********************** 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  : 0.690 
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: 0.7609 (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: 0.7670 (mmm) cc_final: 0.7310 (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: 0.7957 (pp)
  outliers start: 4
  outliers final: 1
  residues processed: 194
  average time/residue: 0.1658
  time to fit residues: 43.7689
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  : 0.690 
-------------------------------------------------------------------------------
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 75 optimal weight:    0.0670
   chunk 68 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 23 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.6118

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.140898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.113101 restraints weight = 9498.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.116405 restraints weight = 5812.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.118473 restraints weight = 4240.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6896  Z= 0.195
  Angle     :  0.628   9.253   9358  Z= 0.312
  Chirality :  0.041   0.154   1102
  Planarity :  0.005   0.057   1175
  Dihedral  :  5.374  29.903    964
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.66 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.26), residues: 896
  helix: -1.46 (0.18), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.37 (0.38), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 291 
 HIS   0.006   0.001   HIS B 284 
 PHE   0.023   0.001   PHE B  92 
 TYR   0.007   0.001   TYR A 100 
 ARG   0.007   0.001   ARG B  98 

*********************** 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
  201 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8395 (t80) cc_final: 0.8034 (t80)
REVERT: A  132 PHE cc_start: 0.8169 (t80) cc_final: 0.7850 (t80)
REVERT: A  210 TYR cc_start: 0.8363 (t80) cc_final: 0.7946 (t80)
REVERT: A  228 MET cc_start: 0.8579 (tpp) cc_final: 0.7975 (mmt)
REVERT: A  253 TRP cc_start: 0.8159 (p-90) cc_final: 0.7575 (p-90)
REVERT: A  421 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8097 (pp)
REVERT: A  459 GLU cc_start: 0.7523 (mp0) cc_final: 0.6994 (mp0)
REVERT: B   91 MET cc_start: 0.8247 (mtm) cc_final: 0.7945 (mtm)
REVERT: B  100 TYR cc_start: 0.8318 (m-80) cc_final: 0.7860 (m-80)
REVERT: B  228 MET cc_start: 0.7810 (mmm) cc_final: 0.7529 (mmm)
REVERT: B  264 ILE cc_start: 0.8657 (tt) cc_final: 0.8425 (tt)
REVERT: B  284 HIS cc_start: 0.8280 (p-80) cc_final: 0.7970 (p90)
REVERT: B  335 PHE cc_start: 0.8726 (t80) cc_final: 0.8500 (t80)
REVERT: B  421 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7761 (pp)
  outliers start: 25
  outliers final: 14
  residues processed: 186
  average time/residue: 0.1484
  time to fit residues: 39.1194
Evaluate side-chains
  165 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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 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 5 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  70 HIS
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
B  63 GLN
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.136657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.108769 restraints weight = 9640.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.111943 restraints weight = 5917.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.114055 restraints weight = 4340.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6896  Z= 0.238
  Angle     :  0.628   9.192   9358  Z= 0.312
  Chirality :  0.043   0.165   1102
  Planarity :  0.005   0.052   1175
  Dihedral  :  5.060  28.852    962
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 19.50 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.28), residues: 896
  helix: -0.78 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.99 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 291 
 HIS   0.005   0.001   HIS B 284 
 PHE   0.013   0.001   PHE A 348 
 TYR   0.008   0.001   TYR B 100 
 ARG   0.003   0.000   ARG A  98 

*********************** 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
  184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8463 (t80) cc_final: 0.8124 (t80)
REVERT: A  132 PHE cc_start: 0.8212 (t80) cc_final: 0.7891 (t80)
REVERT: A  210 TYR cc_start: 0.8368 (t80) cc_final: 0.7950 (t80)
REVERT: A  253 TRP cc_start: 0.8222 (p-90) cc_final: 0.7640 (p-90)
REVERT: A  332 MET cc_start: 0.6851 (ttm) cc_final: 0.6610 (ttp)
REVERT: A  421 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8192 (pp)
REVERT: A  459 GLU cc_start: 0.7618 (mp0) cc_final: 0.7125 (mp0)
REVERT: B   91 MET cc_start: 0.8305 (mtm) cc_final: 0.7967 (mtm)
REVERT: B  100 TYR cc_start: 0.8364 (m-80) cc_final: 0.7838 (m-80)
REVERT: B  228 MET cc_start: 0.7909 (mmm) cc_final: 0.7511 (mmm)
REVERT: B  264 ILE cc_start: 0.8739 (tt) cc_final: 0.8510 (tt)
REVERT: B  335 PHE cc_start: 0.8753 (t80) cc_final: 0.8431 (t80)
REVERT: B  421 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7752 (pp)
  outliers start: 31
  outliers final: 17
  residues processed: 166
  average time/residue: 0.1472
  time to fit residues: 35.1178
Evaluate side-chains
  166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
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  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 36 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 58 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0010
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.4786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
B  63 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.140107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.112969 restraints weight = 9674.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.116055 restraints weight = 5852.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.118484 restraints weight = 4277.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6896  Z= 0.177
  Angle     :  0.594   9.714   9358  Z= 0.295
  Chirality :  0.041   0.134   1102
  Planarity :  0.004   0.049   1175
  Dihedral  :  4.877  29.319    962
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.45 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.29), residues: 896
  helix: -0.38 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.78 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  59 
 HIS   0.003   0.000   HIS B 284 
 PHE   0.022   0.001   PHE B  92 
 TYR   0.025   0.001   TYR B 419 
 ARG   0.009   0.000   ARG A  18 

*********************** 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
  181 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A   92 PHE cc_start: 0.8406 (t80) cc_final: 0.8078 (t80)
REVERT: A   98 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8289 (tpp80)
REVERT: A  210 TYR cc_start: 0.8349 (t80) cc_final: 0.7975 (t80)
REVERT: A  228 MET cc_start: 0.8417 (mmm) cc_final: 0.7949 (mmt)
REVERT: A  253 TRP cc_start: 0.8187 (p-90) cc_final: 0.7610 (p-90)
REVERT: A  421 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8200 (pp)
REVERT: A  438 PHE cc_start: 0.7638 (m-10) cc_final: 0.6907 (t80)
REVERT: A  459 GLU cc_start: 0.7603 (mp0) cc_final: 0.7183 (mp0)
REVERT: B   20 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7733 (tm-30)
REVERT: B   91 MET cc_start: 0.8281 (mtm) cc_final: 0.7971 (mtm)
REVERT: B  100 TYR cc_start: 0.8289 (m-80) cc_final: 0.7763 (m-80)
REVERT: B  264 ILE cc_start: 0.8710 (tt) cc_final: 0.8477 (tt)
REVERT: B  335 PHE cc_start: 0.8697 (t80) cc_final: 0.8409 (t80)
REVERT: B  421 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7730 (pp)
  outliers start: 24
  outliers final: 18
  residues processed: 170
  average time/residue: 0.1374
  time to fit residues: 33.8936
Evaluate side-chains
  167 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 63 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.138059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.110524 restraints weight = 9689.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.113688 restraints weight = 5978.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.115650 restraints weight = 4405.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6896  Z= 0.242
  Angle     :  0.620   9.986   9358  Z= 0.306
  Chirality :  0.043   0.159   1102
  Planarity :  0.004   0.048   1175
  Dihedral  :  4.838  28.603    962
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 22.75 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.29), residues: 896
  helix: -0.28 (0.21), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.64 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A  59 
 HIS   0.003   0.001   HIS B 284 
 PHE   0.013   0.001   PHE A 348 
 TYR   0.009   0.001   TYR B 419 
 ARG   0.003   0.000   ARG B  64 

*********************** 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
  179 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8425 (t80) cc_final: 0.8139 (t80)
REVERT: A   98 ARG cc_start: 0.8703 (tpp-160) cc_final: 0.8407 (tpp80)
REVERT: A  210 TYR cc_start: 0.8367 (t80) cc_final: 0.7993 (t80)
REVERT: A  253 TRP cc_start: 0.8269 (p-90) cc_final: 0.7707 (p-90)
REVERT: A  421 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8146 (pp)
REVERT: A  438 PHE cc_start: 0.7719 (m-10) cc_final: 0.6943 (t80)
REVERT: A  459 GLU cc_start: 0.7652 (mp0) cc_final: 0.7205 (mp0)
REVERT: B   20 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: B  100 TYR cc_start: 0.8292 (m-80) cc_final: 0.7789 (m-80)
REVERT: B  335 PHE cc_start: 0.8693 (t80) cc_final: 0.8419 (t80)
REVERT: B  421 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7794 (pp)
  outliers start: 31
  outliers final: 21
  residues processed: 167
  average time/residue: 0.1288
  time to fit residues: 31.8448
Evaluate side-chains
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
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  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  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  168 LEU
Chi-restraints excluded: chain B residue  171 ASP
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  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 20 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.136768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.109322 restraints weight = 9673.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.112465 restraints weight = 5973.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.114416 restraints weight = 4400.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6896  Z= 0.265
  Angle     :  0.635  10.099   9358  Z= 0.315
  Chirality :  0.043   0.150   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.863  28.843    962
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 23.34 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.29), residues: 896
  helix: -0.22 (0.21), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.53 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  59 
 HIS   0.003   0.001   HIS B 284 
 PHE   0.014   0.001   PHE A 348 
 TYR   0.012   0.001   TYR B 419 
 ARG   0.002   0.000   ARG A  98 

*********************** 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
  174 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8391 (t80) cc_final: 0.8119 (t80)
REVERT: A   98 ARG cc_start: 0.8735 (tpp-160) cc_final: 0.8535 (tpp80)
REVERT: A  210 TYR cc_start: 0.8436 (t80) cc_final: 0.8089 (t80)
REVERT: A  253 TRP cc_start: 0.8363 (p-90) cc_final: 0.7762 (p-90)
REVERT: A  421 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8158 (pp)
REVERT: A  438 PHE cc_start: 0.7711 (m-10) cc_final: 0.6953 (t80)
REVERT: A  459 GLU cc_start: 0.7685 (mp0) cc_final: 0.7308 (mp0)
REVERT: B   20 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7750 (tm-30)
REVERT: B   36 LEU cc_start: 0.9027 (mt) cc_final: 0.8686 (tp)
REVERT: B  100 TYR cc_start: 0.8383 (m-80) cc_final: 0.7805 (m-80)
REVERT: B  335 PHE cc_start: 0.8715 (t80) cc_final: 0.8436 (t80)
REVERT: B  421 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7786 (pp)
  outliers start: 31
  outliers final: 25
  residues processed: 161
  average time/residue: 0.1346
  time to fit residues: 31.8767
Evaluate side-chains
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
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  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  434 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0870
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.139138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.111828 restraints weight = 9631.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.115047 restraints weight = 5890.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.117201 restraints weight = 4311.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6896  Z= 0.188
  Angle     :  0.607  10.450   9358  Z= 0.300
  Chirality :  0.042   0.141   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.784  29.502    962
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.90 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.29), residues: 896
  helix:  0.02 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.58 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  59 
 HIS   0.004   0.001   HIS B 284 
 PHE   0.024   0.001   PHE B  92 
 TYR   0.010   0.001   TYR B 419 
 ARG   0.003   0.000   ARG B  64 

*********************** 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
  177 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8317 (t80) cc_final: 0.8007 (t80)
REVERT: A  210 TYR cc_start: 0.8438 (t80) cc_final: 0.8105 (t80)
REVERT: A  253 TRP cc_start: 0.8313 (p-90) cc_final: 0.7678 (p-90)
REVERT: A  421 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8199 (pp)
REVERT: A  438 PHE cc_start: 0.7597 (m-10) cc_final: 0.6864 (t80)
REVERT: A  459 GLU cc_start: 0.7609 (mp0) cc_final: 0.7259 (mp0)
REVERT: B   20 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: B   36 LEU cc_start: 0.8982 (mt) cc_final: 0.8647 (tp)
REVERT: B  100 TYR cc_start: 0.8316 (m-80) cc_final: 0.7778 (m-80)
REVERT: B  128 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8347 (tt)
REVERT: B  228 MET cc_start: 0.7960 (mmm) cc_final: 0.7635 (mmm)
REVERT: B  335 PHE cc_start: 0.8701 (t80) cc_final: 0.8396 (t80)
REVERT: B  421 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7706 (pp)
  outliers start: 33
  outliers final: 20
  residues processed: 162
  average time/residue: 0.1311
  time to fit residues: 31.5504
Evaluate side-chains
  164 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
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  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  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 14 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0670
   chunk 58 optimal weight:    0.2980
   chunk 47 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3490 r_free = 0.3490 target = 0.140095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.113070 restraints weight = 9549.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.116332 restraints weight = 5821.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118329 restraints weight = 4232.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6896  Z= 0.184
  Angle     :  0.611  10.535   9358  Z= 0.303
  Chirality :  0.042   0.155   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.717  29.049    962
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 24.08 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.29), residues: 896
  helix:  0.15 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.56 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  59 
 HIS   0.004   0.000   HIS B 284 
 PHE   0.014   0.001   PHE A  83 
 TYR   0.009   0.001   TYR B 419 
 ARG   0.006   0.000   ARG A  98 

*********************** 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
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8328 (t80) cc_final: 0.8034 (t80)
REVERT: A  210 TYR cc_start: 0.8429 (t80) cc_final: 0.8109 (t80)
REVERT: A  253 TRP cc_start: 0.8241 (p-90) cc_final: 0.7628 (p-90)
REVERT: A  421 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8232 (pp)
REVERT: A  438 PHE cc_start: 0.7508 (m-10) cc_final: 0.6802 (t80)
REVERT: A  459 GLU cc_start: 0.7588 (mp0) cc_final: 0.7279 (mp0)
REVERT: B   20 GLN cc_start: 0.8491 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: B   36 LEU cc_start: 0.8976 (mt) cc_final: 0.8647 (tp)
REVERT: B  100 TYR cc_start: 0.8301 (m-80) cc_final: 0.7781 (m-80)
REVERT: B  128 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8332 (tt)
REVERT: B  228 MET cc_start: 0.7923 (mmm) cc_final: 0.7605 (mmm)
REVERT: B  421 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7731 (pp)
  outliers start: 28
  outliers final: 22
  residues processed: 156
  average time/residue: 0.1264
  time to fit residues: 29.4918
Evaluate side-chains
  166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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  288 ILE
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  434 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  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 4 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0370
   chunk 36 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.8464

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.139462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.112100 restraints weight = 9675.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.115346 restraints weight = 5885.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.117536 restraints weight = 4295.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6896  Z= 0.215
  Angle     :  0.619  10.569   9358  Z= 0.305
  Chirality :  0.042   0.154   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.707  28.733    962
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 23.93 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.29), residues: 896
  helix:  0.22 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.40 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 291 
 HIS   0.004   0.001   HIS B 284 
 PHE   0.023   0.001   PHE B  92 
 TYR   0.007   0.001   TYR B 100 
 ARG   0.005   0.000   ARG A  98 

*********************** 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
  167 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8318 (t80) cc_final: 0.8005 (t80)
REVERT: A  210 TYR cc_start: 0.8454 (t80) cc_final: 0.8135 (t80)
REVERT: A  253 TRP cc_start: 0.8338 (p-90) cc_final: 0.7727 (p-90)
REVERT: A  421 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8265 (pp)
REVERT: A  438 PHE cc_start: 0.7472 (m-10) cc_final: 0.6785 (t80)
REVERT: A  459 GLU cc_start: 0.7592 (mp0) cc_final: 0.7278 (mp0)
REVERT: B   20 GLN cc_start: 0.8508 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: B   36 LEU cc_start: 0.8981 (mt) cc_final: 0.8673 (tp)
REVERT: B  100 TYR cc_start: 0.8314 (m-80) cc_final: 0.7794 (m-80)
REVERT: B  128 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8332 (tt)
REVERT: B  228 MET cc_start: 0.7926 (mmm) cc_final: 0.7602 (mmm)
REVERT: B  335 PHE cc_start: 0.8738 (t80) cc_final: 0.8428 (t80)
REVERT: B  421 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7735 (pp)
  outliers start: 28
  outliers final: 23
  residues processed: 154
  average time/residue: 0.1279
  time to fit residues: 29.5478
Evaluate side-chains
  166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
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  288 ILE
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  434 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  280 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.139740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.112422 restraints weight = 9779.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.115695 restraints weight = 5924.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.117865 restraints weight = 4304.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6896  Z= 0.215
  Angle     :  0.623  10.566   9358  Z= 0.308
  Chirality :  0.042   0.147   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.705  28.481    962
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 24.67 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.30), residues: 896
  helix:  0.33 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.44 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 
 PHE   0.010   0.001   PHE A 348 
 TYR   0.007   0.001   TYR B 100 
 ARG   0.005   0.000   ARG A  98 

********************** 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
  172 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8372 (t80) cc_final: 0.8074 (t80)
REVERT: A  210 TYR cc_start: 0.8457 (t80) cc_final: 0.8143 (t80)
REVERT: A  253 TRP cc_start: 0.8341 (p-90) cc_final: 0.7732 (p-90)
REVERT: A  421 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8259 (pp)
REVERT: A  438 PHE cc_start: 0.7434 (m-10) cc_final: 0.6764 (t80)
REVERT: A  459 GLU cc_start: 0.7582 (mp0) cc_final: 0.7296 (mp0)
REVERT: B   20 GLN cc_start: 0.8502 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: B   36 LEU cc_start: 0.8970 (mt) cc_final: 0.8661 (tp)
REVERT: B  100 TYR cc_start: 0.8316 (m-80) cc_final: 0.7816 (m-80)
REVERT: B  128 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8326 (tt)
REVERT: B  228 MET cc_start: 0.7931 (mmm) cc_final: 0.7610 (mmm)
REVERT: B  335 PHE cc_start: 0.8718 (t80) cc_final: 0.8409 (t80)
REVERT: B  421 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7730 (pp)
  outliers start: 29
  outliers final: 21
  residues processed: 159
  average time/residue: 0.1334
  time to fit residues: 31.5301
Evaluate side-chains
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  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  434 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  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 11 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.140479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.113256 restraints weight = 9670.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.116473 restraints weight = 5864.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.118484 restraints weight = 4270.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6896  Z= 0.203
  Angle     :  0.618  10.469   9358  Z= 0.306
  Chirality :  0.042   0.140   1102
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.681  28.685    962
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.96 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.30), residues: 896
  helix:  0.39 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.39 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 
 PHE   0.033   0.001   PHE B  92 
 TYR   0.007   0.001   TYR B 100 
 ARG   0.006   0.000   ARG A  98 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2071.73 seconds
wall clock time: 36 minutes 48.77 seconds (2208.77 seconds total)