Starting phenix.real_space_refine
on Tue May 13 08:58:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k8t_36961/05_2025/8k8t_36961.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k8t_36961/05_2025/8k8t_36961.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k8t_36961/05_2025/8k8t_36961.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k8t_36961/05_2025/8k8t_36961.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k8t_36961/05_2025/8k8t_36961.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k8t_36961/05_2025/8k8t_36961.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.971
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      82      5.16       5
     C    6280      2.51       5
     N    1706      2.21       5
     O    1858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9926
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 3719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3719
          Classifications: {'peptide': 450}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 442}
          Chain breaks: 7
    Chain: "D"
      Number of atoms: 3735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3735
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 6, 'TRANS': 445}
          Chain breaks: 6
    Chain: "K"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1236
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 1, 'TRANS': 152}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1236
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 1, 'TRANS': 152}
          Chain breaks: 1
  Time building chain proxies: 8.57, per 1000 atoms: 0.86
  Number of scatterers: 9926
  At special positions: 0
  Unit cell: (138.749, 158.453, 103.446, 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      82     16.00
     O    1858      8.00
     N    1706      7.00
     C    6280      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.78
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2332

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 4 sheets defined
      77.1% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'C' and resid 29 through 46
      removed outlier: 3.557A  pdb=" N   LEU C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 52
      removed outlier: 3.760A  pdb=" N   GLY C  51 " --> pdb=" O   ASN C  48 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU C  52 " --> pdb=" O   ASN C  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 48 through 52'
    Processing helix  chain 'C' and resid 53 through 67
    Processing helix  chain 'C' and resid 69 through 87
      removed outlier: 3.511A  pdb=" N   LEU C  73 " --> pdb=" O   HIS C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 95
    Processing helix  chain 'C' and resid 103 through 123
    Processing helix  chain 'C' and resid 125 through 130
    Processing helix  chain 'C' and resid 138 through 151
    Processing helix  chain 'C' and resid 156 through 174
    Processing helix  chain 'C' and resid 179 through 193
      removed outlier: 3.527A  pdb=" N   ILE C 183 " --> pdb=" O   ASP C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 205
    Processing helix  chain 'C' and resid 205 through 225
      removed outlier: 3.670A  pdb=" N   LEU C 225 " --> pdb=" O   SER C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 252
    Processing helix  chain 'C' and resid 256 through 268
    Processing helix  chain 'C' and resid 272 through 277
    Processing helix  chain 'C' and resid 292 through 304
      removed outlier: 3.986A  pdb=" N   MET C 299 " --> pdb=" O   ASP C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 330
      removed outlier: 3.963A  pdb=" N   THR C 312 " --> pdb=" O   ASN C 308 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   MET C 313 " --> pdb=" O   GLY C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 359
      removed outlier: 3.763A  pdb=" N   ILE C 342 " --> pdb=" O   PRO C 338 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU C 356 " --> pdb=" O   PHE C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 363 through 378
    Processing helix  chain 'C' and resid 383 through 397
      removed outlier: 3.918A  pdb=" N   ILE C 392 " --> pdb=" O   LEU C 388 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP C 393 " --> pdb=" O   SER C 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 422
      removed outlier: 3.708A  pdb=" N   LEU C 418 " --> pdb=" O   LYS C 414 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE C 421 " --> pdb=" O   VAL C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 431 through 439
      removed outlier: 4.097A  pdb=" N   ARG C 438 " --> pdb=" O   GLN C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 447 through 459
      removed outlier: 3.537A  pdb=" N   GLU C 451 " --> pdb=" O   SER C 447 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS C 452 " --> pdb=" O   ASP C 448 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE C 455 " --> pdb=" O   GLU C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 465 through 480
      removed outlier: 3.796A  pdb=" N   LYS C 469 " --> pdb=" O   GLN C 465 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   LEU C 470 " --> pdb=" O   PHE C 466 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   MET C 473 " --> pdb=" O   LYS C 469 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   PHE C 474 " --> pdb=" O   LEU C 470 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   MET C 477 " --> pdb=" O   MET C 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 46
    Processing helix  chain 'D' and resid 48 through 52
      removed outlier: 3.713A  pdb=" N   GLY D  51 " --> pdb=" O   ASN D  48 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU D  52 " --> pdb=" O   ASN D  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 48 through 52'
    Processing helix  chain 'D' and resid 53 through 68
    Processing helix  chain 'D' and resid 69 through 87
    Processing helix  chain 'D' and resid 89 through 95
    Processing helix  chain 'D' and resid 102 through 123
    Processing helix  chain 'D' and resid 125 through 130
    Processing helix  chain 'D' and resid 138 through 151
    Processing helix  chain 'D' and resid 156 through 174
    Processing helix  chain 'D' and resid 180 through 193
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 205 through 225
      removed outlier: 3.543A  pdb=" N   LEU D 225 " --> pdb=" O   SER D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 251
    Processing helix  chain 'D' and resid 253 through 255
      No H-bonds generated for 'chain 'D' and resid 253 through 255'
    Processing helix  chain 'D' and resid 256 through 268
      removed outlier: 3.678A  pdb=" N   VAL D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 271
      No H-bonds generated for 'chain 'D' and resid 269 through 271'
    Processing helix  chain 'D' and resid 272 through 278
      removed outlier: 3.520A  pdb=" N   ILE D 276 " --> pdb=" O   HIS D 272 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU D 278 " --> pdb=" O   LYS D 274 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 304
      removed outlier: 3.501A  pdb=" N   LEU D 296 " --> pdb=" O   LYS D 292 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   MET D 299 " --> pdb=" O   ASP D 295 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 330
      removed outlier: 3.896A  pdb=" N   THR D 312 " --> pdb=" O   ASN D 308 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   MET D 313 " --> pdb=" O   GLY D 309 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 359
      removed outlier: 3.998A  pdb=" N   ILE D 342 " --> pdb=" O   PRO D 338 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE D 355 " --> pdb=" O   ARG D 351 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU D 356 " --> pdb=" O   PHE D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 363 through 381
      removed outlier: 4.130A  pdb=" N   ASN D 379 " --> pdb=" O   GLU D 375 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN D 381 " --> pdb=" O   PHE D 377 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 383 through 397
      removed outlier: 3.839A  pdb=" N   ILE D 392 " --> pdb=" O   LEU D 388 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 422
      removed outlier: 3.811A  pdb=" N   LEU D 418 " --> pdb=" O   LYS D 414 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE D 419 " --> pdb=" O   ALA D 415 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG D 420 " --> pdb=" O   MET D 416 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE D 421 " --> pdb=" O   VAL D 417 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 424 through 442
      removed outlier: 3.555A  pdb=" N   PHE D 428 " --> pdb=" O   GLU D 424 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG D 438 " --> pdb=" O   GLN D 434 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   THR D 442 " --> pdb=" O   ARG D 438 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 447 through 459
      removed outlier: 3.635A  pdb=" N   GLU D 451 " --> pdb=" O   SER D 447 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS D 452 " --> pdb=" O   ASP D 448 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ILE D 455 " --> pdb=" O   GLU D 451 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 465 through 480
      removed outlier: 3.845A  pdb=" N   LYS D 469 " --> pdb=" O   GLN D 465 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   LEU D 470 " --> pdb=" O   PHE D 466 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   MET D 473 " --> pdb=" O   LYS D 469 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   PHE D 474 " --> pdb=" O   LEU D 470 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 30 through 47
      removed outlier: 4.392A  pdb=" N   GLN K  34 " --> pdb=" O   ALA K  30 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 66 through 70
      removed outlier: 3.917A  pdb=" N   ALA K  70 " --> pdb=" O   LEU K  67 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 72 through 80
    Processing helix  chain 'K' and resid 97 through 111
    Processing helix  chain 'K' and resid 122 through 131
    Processing helix  chain 'K' and resid 132 through 146
    Processing helix  chain 'K' and resid 151 through 163
      removed outlier: 3.663A  pdb=" N   VAL K 155 " --> pdb=" O   ASN K 151 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 164 through 178
    Processing helix  chain 'L' and resid 30 through 47
      removed outlier: 4.511A  pdb=" N   GLN L  34 " --> pdb=" O   ALA L  30 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 66 through 71
      removed outlier: 3.748A  pdb=" N   SER L  71 " --> pdb=" O   LEU L  67 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 72 through 80
    Processing helix  chain 'L' and resid 97 through 111
    Processing helix  chain 'L' and resid 122 through 131
    Processing helix  chain 'L' and resid 132 through 146
    Processing helix  chain 'L' and resid 151 through 163
      removed outlier: 3.670A  pdb=" N   VAL L 155 " --> pdb=" O   ASN L 151 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 164 through 178
    Processing sheet with id=AA1, first strand: chain 'K' and resid 25 through 28
      removed outlier: 4.217A  pdb=" N   ASN K  25 " --> pdb=" O   LEU L 115 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU L 115 " --> pdb=" O   ASN K  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 60 through 63
    Processing sheet with id=AA3, first strand: chain 'K' and resid 112 through 113
    Processing sheet with id=AA4, first strand: chain 'L' and resid 60 through 63

    630 hydrogen bonds defined for protein.
    1878 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.50: 5728
        1.50 -     1.78: 4203
        1.78 -     2.07: 135
        2.07 -     2.35: 0
        2.35 -     2.63: 1
  Bond restraints: 10067
  Sorted by residual:
  bond pdb=" C   LYS C 174 "
       pdb=" N   GLU C 176 "
    ideal  model  delta    sigma   weight residual
    1.329  2.633 -1.304 1.40e-02 5.10e+03 8.68e+03
  bond pdb=" N   ILE K 132 "
       pdb=" CA  ILE K 132 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 7.30e-03 1.88e+04 2.14e+01
  bond pdb=" N   VAL L  91 "
       pdb=" CA  VAL L  91 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.15e-02 7.56e+03 1.09e+01
  bond pdb=" N   VAL C 178 "
       pdb=" CA  VAL C 178 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.23e-02 6.61e+03 1.07e+01
  bond pdb=" N   VAL K  96 "
       pdb=" CA  VAL K  96 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.14e-02 7.69e+03 1.06e+01
  ... (remaining 10062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.43: 13494
        6.43 -    12.86: 10
       12.86 -    19.29: 0
       19.29 -    25.72: 2
       25.72 -    32.15: 1
  Bond angle restraints: 13507
  Sorted by residual:
  angle pdb=" C   LYS C 174 "
        pdb=" N   GLU C 176 "
        pdb=" CA  GLU C 176 "
      ideal   model   delta    sigma   weight residual
     121.70  153.85  -32.15 1.80e+00 3.09e-01 3.19e+02
  angle pdb=" O   LYS C 174 "
        pdb=" C   LYS C 174 "
        pdb=" N   GLU C 176 "
      ideal   model   delta    sigma   weight residual
     122.59   99.28   23.31 1.33e+00 5.65e-01 3.07e+02
  angle pdb=" CA  LYS C 174 "
        pdb=" C   LYS C 174 "
        pdb=" N   GLU C 176 "
      ideal   model   delta    sigma   weight residual
     116.84  137.15  -20.31 1.71e+00 3.42e-01 1.41e+02
  angle pdb=" N   LEU C 380 "
        pdb=" CA  LEU C 380 "
        pdb=" C   LEU C 380 "
      ideal   model   delta    sigma   weight residual
     113.19  107.31    5.88 1.19e+00 7.06e-01 2.44e+01
  angle pdb=" CA  GLU K 169 "
        pdb=" CB  GLU K 169 "
        pdb=" CG  GLU K 169 "
      ideal   model   delta    sigma   weight residual
     114.10  122.07   -7.97 2.00e+00 2.50e-01 1.59e+01
  ... (remaining 13502 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 5114
       16.41 -    32.81: 730
       32.81 -    49.22: 220
       49.22 -    65.62: 98
       65.62 -    82.03: 17
  Dihedral angle restraints: 6179
    sinusoidal: 2610
      harmonic: 3569
  Sorted by residual:
  dihedral pdb=" CA  GLN L 121 "
           pdb=" C   GLN L 121 "
           pdb=" N   GLU L 122 "
           pdb=" CA  GLU L 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.72   21.28     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  LYS D  88 "
           pdb=" C   LYS D  88 "
           pdb=" N   VAL D  89 "
           pdb=" CA  VAL D  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.60   16.40     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  GLN K 121 "
           pdb=" C   GLN K 121 "
           pdb=" N   GLU K 122 "
           pdb=" CA  GLU K 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.66   16.34     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 6176 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 940
       0.040 -    0.081: 368
       0.081 -    0.121: 140
       0.121 -    0.162: 54
       0.162 -    0.202: 13
  Chirality restraints: 1515
  Sorted by residual:
  chirality pdb=" CA  ILE L  93 "
            pdb=" N   ILE L  93 "
            pdb=" C   ILE L  93 "
            pdb=" CB  ILE L  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  VAL D 427 "
            pdb=" N   VAL D 427 "
            pdb=" C   VAL D 427 "
            pdb=" CB  VAL D 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.27e-01
  chirality pdb=" CA  ILE K 132 "
            pdb=" N   ILE K 132 "
            pdb=" C   ILE K 132 "
            pdb=" CB  ILE K 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.79e-01
  ... (remaining 1512 not shown)

  Planarity restraints: 1726
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 174 "   -0.076 2.00e-02 2.50e+03   1.03e-01 1.06e+02
        pdb=" C   LYS C 174 "    0.177 2.00e-02 2.50e+03
        pdb=" O   LYS C 174 "   -0.062 2.00e-02 2.50e+03
        pdb=" N   GLU C 176 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 430 "   -0.247 9.50e-02 1.11e+02   1.11e-01 7.57e+00
        pdb=" NE  ARG D 430 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 430 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 430 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 430 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 247 "    0.218 9.50e-02 1.11e+02   9.77e-02 5.88e+00
        pdb=" NE  ARG C 247 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 247 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 247 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 247 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1723 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 938
        2.74 -     3.28: 10831
        3.28 -     3.82: 17194
        3.82 -     4.36: 19998
        4.36 -     4.90: 32396
  Nonbonded interactions: 81357
  Sorted by model distance:
  nonbonded pdb=" O   GLU D 407 "
            pdb=" OG1 THR D 410 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" NH1 ARG D  90 "
            pdb=" OE1 GLN D 150 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OE2 GLU D 206 "
            pdb=" OG1 THR D 256 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" N   GLU L 150 "
            pdb=" OE1 GLU L 150 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" N   GLU D 137 "
            pdb=" OE1 GLU D 137 "
     model   vdw
     2.243 3.120
  ... (remaining 81352 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 'C'
  selection = (chain 'D' and (resid 14 through 426 or resid 428 or resid 430 through 482))
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

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:             10.540
  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:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     27.650
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
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      :  0.014   1.304  10067  Z= 1.016
  Angle     :  0.972  32.148  13507  Z= 0.638
  Chirality :  0.055   0.202   1515
  Planarity :  0.007   0.111   1726
  Dihedral  : 18.585  82.031   3847
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 29.86 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1171
  helix:  0.79 (0.18), residues: 839
  sheet:  None (None), residues: 0
  loop : -0.74 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  34 
 HIS   0.005   0.001   HIS C 250 
 PHE   0.038   0.002   PHE C 224 
 TYR   0.018   0.002   TYR D 320 
 ARG   0.005   0.001   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16639 (  630)
  hydrogen bonds       : angle       6.55528 ( 1878)
  covalent geometry    : bond        0.01434 (10067)
  covalent geometry    : angle       0.97167 (13507)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 355
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  168 MET cc_start: 0.7565 (mtp) cc_final: 0.7287 (mtt)
REVERT: C  246 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6511 (mm-30)
REVERT: C  258 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7072 (mm-30)
REVERT: C  262 LYS cc_start: 0.7356 (mmtm) cc_final: 0.6739 (mmtm)
REVERT: C  267 GLU cc_start: 0.7734 (tp30) cc_final: 0.7362 (tp30)
REVERT: C  279 MET cc_start: 0.6129 (mtm) cc_final: 0.5725 (ptt)
REVERT: C  315 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6955 (mp0)
REVERT: C  317 MET cc_start: 0.7411 (ttp) cc_final: 0.7148 (ptm)
REVERT: C  326 LYS cc_start: 0.8131 (tptp) cc_final: 0.7677 (tptp)
REVERT: D   78 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7815 (ttm-80)
REVERT: D  128 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7621 (mmm-85)
REVERT: D  167 ASP cc_start: 0.7311 (m-30) cc_final: 0.7073 (m-30)
REVERT: D  180 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8299 (ttm170)
REVERT: D  267 GLU cc_start: 0.7942 (tp30) cc_final: 0.7390 (tp30)
REVERT: D  315 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7120 (mm-30)
REVERT: D  438 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8013 (mmm-85)
REVERT: D  450 SER cc_start: 0.8024 (m) cc_final: 0.7740 (p)
REVERT: K   27 TYR cc_start: 0.8413 (m-10) cc_final: 0.8048 (m-10)
REVERT: K   92 LEU cc_start: 0.7803 (mm) cc_final: 0.7579 (mt)
REVERT: L   38 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7354 (mtm-85)
REVERT: L   73 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6412 (p0)
  outliers start: 31
  outliers final: 10
  residues processed: 368
  average time/residue: 0.2719
  time to fit residues: 133.1100
Evaluate side-chains
  349 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 337
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue  171 ARG
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue  222 GLN
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain L residue   73 ASP
Chi-restraints excluded: chain L residue  136 ILE
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 94 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 70 optimal weight:    0.1980
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
C 163 GLN
C 188 GLN
C 435 HIS
D  60 ASN
** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.144036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.129787 restraints weight = 18915.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.133509 restraints weight = 9140.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.135872 restraints weight = 5212.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10067  Z= 0.163
  Angle     :  0.671  20.663  13507  Z= 0.357
  Chirality :  0.041   0.307   1515
  Planarity :  0.004   0.038   1726
  Dihedral  :  5.727  72.433   1346
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.26 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 25.63 %
    Favored  : 68.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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:  0.84 (0.25), residues: 1173
  helix:  1.10 (0.18), residues: 877
  sheet:  None (None), residues: 0
  loop : -0.91 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K 146 
 HIS   0.003   0.001   HIS D 112 
 PHE   0.025   0.002   PHE C 377 
 TYR   0.017   0.002   TYR D  29 
 ARG   0.006   0.001   ARG D  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04576 (  630)
  hydrogen bonds       : angle       4.82684 ( 1878)
  covalent geometry    : bond        0.00342 (10067)
  covalent geometry    : angle       0.67078 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  404 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 343
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7557 (mm-30)
REVERT: C   64 MET cc_start: 0.8039 (tpp) cc_final: 0.7688 (tpp)
REVERT: C   83 GLU cc_start: 0.7681 (tp30) cc_final: 0.7163 (tp30)
REVERT: C  159 ASP cc_start: 0.7119 (t0) cc_final: 0.6572 (t70)
REVERT: C  163 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6597 (mp10)
REVERT: C  191 MET cc_start: 0.7950 (mtt) cc_final: 0.7721 (mtt)
REVERT: C  224 PHE cc_start: 0.7012 (m-80) cc_final: 0.6785 (m-80)
REVERT: C  243 GLU cc_start: 0.7604 (tp30) cc_final: 0.7281 (tp30)
REVERT: C  246 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6477 (mm-30)
REVERT: C  258 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7182 (mm-30)
REVERT: C  262 LYS cc_start: 0.7455 (mmtm) cc_final: 0.6884 (mmtm)
REVERT: C  315 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6918 (mp0)
REVERT: C  326 LYS cc_start: 0.8073 (tptp) cc_final: 0.7666 (tptp)
REVERT: C  434 GLN cc_start: 0.7560 (tp40) cc_final: 0.7351 (tp40)
REVERT: C  438 ARG cc_start: 0.7756 (mmt90) cc_final: 0.7536 (mmt90)
REVERT: D   47 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7974 (mmmt)
REVERT: D   62 TYR cc_start: 0.6537 (t80) cc_final: 0.6275 (t80)
REVERT: D   64 MET cc_start: 0.7036 (mtp) cc_final: 0.6765 (mtp)
REVERT: D   78 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7755 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7582 (tp30) cc_final: 0.7291 (tp30)
REVERT: D  128 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7585 (mmm-85)
REVERT: D  167 ASP cc_start: 0.7453 (m-30) cc_final: 0.7172 (m-30)
REVERT: D  203 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6559 (mp0)
REVERT: D  267 GLU cc_start: 0.7664 (tp30) cc_final: 0.7132 (tp30)
REVERT: D  367 LYS cc_start: 0.8210 (tptt) cc_final: 0.7747 (tptt)
REVERT: D  416 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6232 (mmm)
REVERT: D  424 GLU cc_start: 0.7470 (mp0) cc_final: 0.7241 (tp30)
REVERT: D  438 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7379 (mmt90)
REVERT: D  442 THR cc_start: 0.6921 (OUTLIER) cc_final: 0.6383 (t)
REVERT: K   27 TYR cc_start: 0.8350 (m-10) cc_final: 0.8066 (m-10)
REVERT: K   92 LEU cc_start: 0.7724 (mm) cc_final: 0.7504 (mt)
REVERT: L   73 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6460 (p0)
REVERT: L  122 GLU cc_start: 0.6914 (pm20) cc_final: 0.6650 (pm20)
REVERT: L  169 GLU cc_start: 0.7317 (pp20) cc_final: 0.7016 (pp20)
  outliers start: 61
  outliers final: 27
  residues processed: 372
  average time/residue: 0.2558
  time to fit residues: 126.3544
Evaluate side-chains
  361 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 329
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  163 GLN
Chi-restraints excluded: chain C residue  171 ARG
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  308 ASN
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  440 LEU
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  254 LYS
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  342 ILE
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   73 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 113 optimal weight:    0.0870
   chunk 69 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 100 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 82 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.140914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.126542 restraints weight = 18946.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.130239 restraints weight = 9119.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.132550 restraints weight = 5215.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10067  Z= 0.207
  Angle     :  0.665  19.056  13507  Z= 0.358
  Chirality :  0.043   0.318   1515
  Planarity :  0.003   0.032   1726
  Dihedral  :  4.824  49.627   1329
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 27.16 %
    Favored  : 66.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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:  0.78 (0.26), residues: 1173
  helix:  1.06 (0.18), residues: 879
  sheet:  None (None), residues: 0
  loop : -0.98 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L 146 
 HIS   0.005   0.001   HIS D 112 
 PHE   0.019   0.002   PHE C 391 
 TYR   0.016   0.002   TYR D  29 
 ARG   0.005   0.001   ARG D 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04550 (  630)
  hydrogen bonds       : angle       4.67038 ( 1878)
  covalent geometry    : bond        0.00438 (10067)
  covalent geometry    : angle       0.66486 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 348
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7646 (mm-30)
REVERT: C   83 GLU cc_start: 0.7693 (tp30) cc_final: 0.7102 (tp30)
REVERT: C  124 MET cc_start: 0.6805 (tmm) cc_final: 0.6591 (tmm)
REVERT: C  159 ASP cc_start: 0.7768 (t0) cc_final: 0.7316 (t0)
REVERT: C  163 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7330 (mp10)
REVERT: C  173 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7873 (mtt180)
REVERT: C  213 SER cc_start: 0.8467 (t) cc_final: 0.8100 (p)
REVERT: C  218 GLN cc_start: 0.7766 (pp30) cc_final: 0.7415 (pp30)
REVERT: C  258 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7219 (mm-30)
REVERT: C  262 LYS cc_start: 0.7494 (mmtm) cc_final: 0.7260 (mmtm)
REVERT: C  315 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6888 (mp0)
REVERT: C  326 LYS cc_start: 0.8104 (tptp) cc_final: 0.7732 (tptp)
REVERT: C  438 ARG cc_start: 0.7809 (mmt90) cc_final: 0.7525 (mmm-85)
REVERT: D   64 MET cc_start: 0.7352 (mtp) cc_final: 0.6881 (mtp)
REVERT: D   78 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7752 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7594 (tp30) cc_final: 0.7299 (tp30)
REVERT: D   88 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7292 (tppt)
REVERT: D  101 PHE cc_start: 0.8259 (t80) cc_final: 0.8038 (t80)
REVERT: D  125 TYR cc_start: 0.8053 (t80) cc_final: 0.7681 (t80)
REVERT: D  128 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7580 (mmm-85)
REVERT: D  163 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7522 (mm-40)
REVERT: D  167 ASP cc_start: 0.7492 (m-30) cc_final: 0.7183 (m-30)
REVERT: D  203 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6658 (mp0)
REVERT: D  223 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7716 (tmtt)
REVERT: D  267 GLU cc_start: 0.7679 (tp30) cc_final: 0.7167 (tp30)
REVERT: D  299 MET cc_start: 0.7575 (tmm) cc_final: 0.7264 (tmm)
REVERT: D  323 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6682 (tm-30)
REVERT: D  367 LYS cc_start: 0.8202 (tptt) cc_final: 0.7674 (tptt)
REVERT: D  416 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6226 (mmm)
REVERT: D  434 GLN cc_start: 0.7492 (tm-30) cc_final: 0.7195 (tm-30)
REVERT: D  442 THR cc_start: 0.6920 (OUTLIER) cc_final: 0.6380 (t)
REVERT: D  448 ASP cc_start: 0.6648 (m-30) cc_final: 0.6429 (m-30)
REVERT: D  457 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7970 (mmmt)
REVERT: K   27 TYR cc_start: 0.8380 (m-10) cc_final: 0.8161 (m-10)
REVERT: K   85 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6995 (tm-30)
REVERT: L  122 GLU cc_start: 0.6961 (pm20) cc_final: 0.6744 (pm20)
REVERT: L  169 GLU cc_start: 0.7363 (pp20) cc_final: 0.7145 (pp20)
  outliers start: 68
  outliers final: 41
  residues processed: 371
  average time/residue: 0.2448
  time to fit residues: 120.8439
Evaluate side-chains
  388 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 342
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  163 GLN
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  308 ASN
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  426 ASP
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  305 ARG
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  342 ILE
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  454 MET
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    0.1980
   chunk 79 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 115 optimal weight:    0.0970
   chunk 13 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
C 434 GLN
C 435 HIS
D 106 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.140977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.126731 restraints weight = 18750.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.130407 restraints weight = 9040.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.132665 restraints weight = 5181.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10067  Z= 0.183
  Angle     :  0.644  18.790  13507  Z= 0.346
  Chirality :  0.042   0.302   1515
  Planarity :  0.003   0.030   1726
  Dihedral  :  4.562  52.821   1323
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.69 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 30.40 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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:  0.90 (0.26), residues: 1173
  helix:  1.16 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -0.98 (0.40), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L 146 
 HIS   0.004   0.001   HIS C 112 
 PHE   0.031   0.002   PHE D 377 
 TYR   0.032   0.002   TYR D  62 
 ARG   0.004   0.000   ARG L  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 (  630)
  hydrogen bonds       : angle       4.52244 ( 1878)
  covalent geometry    : bond        0.00389 (10067)
  covalent geometry    : angle       0.64369 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 347
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7660 (mm-30)
REVERT: C   62 TYR cc_start: 0.7080 (t80) cc_final: 0.6706 (t80)
REVERT: C   83 GLU cc_start: 0.7640 (tp30) cc_final: 0.7081 (tp30)
REVERT: C   90 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7844 (ttt180)
REVERT: C  124 MET cc_start: 0.6742 (tmm) cc_final: 0.6517 (tmm)
REVERT: C  125 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7720 (t80)
REVERT: C  159 ASP cc_start: 0.7506 (t70) cc_final: 0.7154 (t0)
REVERT: C  163 GLN cc_start: 0.7507 (mp-120) cc_final: 0.7026 (mp10)
REVERT: C  168 MET cc_start: 0.7564 (mtp) cc_final: 0.7302 (ttm)
REVERT: C  173 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7777 (mtt90)
REVERT: C  213 SER cc_start: 0.8401 (t) cc_final: 0.8033 (p)
REVERT: C  218 GLN cc_start: 0.7670 (pp30) cc_final: 0.7343 (pp30)
REVERT: C  315 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6809 (mp0)
REVERT: C  326 LYS cc_start: 0.8092 (tptp) cc_final: 0.7712 (tptp)
REVERT: C  395 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6890 (ttpt)
REVERT: C  438 ARG cc_start: 0.7655 (mmt90) cc_final: 0.7404 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7910 (mmmt)
REVERT: D   46 ARG cc_start: 0.7860 (mtp180) cc_final: 0.7651 (mtm110)
REVERT: D   64 MET cc_start: 0.7309 (mtp) cc_final: 0.6812 (mtp)
REVERT: D   78 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7736 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7650 (tp30) cc_final: 0.7279 (tp30)
REVERT: D   88 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7253 (tppt)
REVERT: D  101 PHE cc_start: 0.8285 (t80) cc_final: 0.8038 (t80)
REVERT: D  125 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7785 (t80)
REVERT: D  163 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7427 (mm-40)
REVERT: D  167 ASP cc_start: 0.7518 (m-30) cc_final: 0.7193 (m-30)
REVERT: D  203 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6601 (mp0)
REVERT: D  212 MET cc_start: 0.7597 (tmm) cc_final: 0.7289 (tmm)
REVERT: D  223 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7696 (tmtt)
REVERT: D  236 LYS cc_start: 0.7961 (tmmt) cc_final: 0.7641 (pttp)
REVERT: D  267 GLU cc_start: 0.7696 (tp30) cc_final: 0.7181 (tp30)
REVERT: D  315 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6911 (mm-30)
REVERT: D  323 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6585 (tm-30)
REVERT: D  367 LYS cc_start: 0.8187 (tptt) cc_final: 0.7651 (tptt)
REVERT: D  416 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6253 (mmm)
REVERT: D  434 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7160 (tm-30)
REVERT: D  442 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6280 (t)
REVERT: D  457 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7940 (mmmt)
REVERT: K   27 TYR cc_start: 0.8397 (m-10) cc_final: 0.8177 (m-10)
REVERT: K   90 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6937 (mp0)
REVERT: K  101 MET cc_start: 0.8259 (mmm) cc_final: 0.8036 (tpt)
REVERT: K  104 ILE cc_start: 0.8680 (tt) cc_final: 0.8473 (tt)
REVERT: K  105 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7849 (mm)
REVERT: K  122 GLU cc_start: 0.6940 (pm20) cc_final: 0.6585 (pm20)
REVERT: L  122 GLU cc_start: 0.6962 (pm20) cc_final: 0.6667 (pm20)
  outliers start: 67
  outliers final: 44
  residues processed: 371
  average time/residue: 0.2594
  time to fit residues: 126.4843
Evaluate side-chains
  388 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 335
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  308 ASN
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  355 PHE
Chi-restraints excluded: chain C residue  395 LYS
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  426 ASP
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  125 TYR
Chi-restraints excluded: chain D residue  254 LYS
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  305 ARG
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  471 GLU
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue   90 GLU
Chi-restraints excluded: chain K residue  105 LEU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  136 ILE
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 163 GLN
** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
D 381 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.138695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.124282 restraints weight = 18431.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.127888 restraints weight = 9101.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.130199 restraints weight = 5275.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10067  Z= 0.243
  Angle     :  0.692  18.878  13507  Z= 0.372
  Chirality :  0.044   0.303   1515
  Planarity :  0.003   0.029   1726
  Dihedral  :  4.740  55.172   1323
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 30.04 %
    Favored  : 62.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1173
  helix:  1.03 (0.18), residues: 875
  sheet:  None (None), residues: 0
  loop : -1.01 (0.40), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP L 146 
 HIS   0.006   0.001   HIS C 112 
 PHE   0.023   0.002   PHE C  21 
 TYR   0.043   0.002   TYR D  62 
 ARG   0.004   0.000   ARG D 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  630)
  hydrogen bonds       : angle       4.59927 ( 1878)
  covalent geometry    : bond        0.00511 (10067)
  covalent geometry    : angle       0.69179 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  439 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 360
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   21 PHE cc_start: 0.7667 (m-10) cc_final: 0.7222 (m-10)
REVERT: C   43 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7654 (mm-30)
REVERT: C   62 TYR cc_start: 0.6908 (t80) cc_final: 0.6564 (t80)
REVERT: C   83 GLU cc_start: 0.7682 (tp30) cc_final: 0.7071 (tp30)
REVERT: C  124 MET cc_start: 0.6873 (tmm) cc_final: 0.6464 (tmm)
REVERT: C  125 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7748 (t80)
REVERT: C  159 ASP cc_start: 0.7547 (t70) cc_final: 0.7101 (t0)
REVERT: C  218 GLN cc_start: 0.7739 (pp30) cc_final: 0.7448 (pp30)
REVERT: C  262 LYS cc_start: 0.7692 (mmtm) cc_final: 0.7440 (mmtm)
REVERT: C  269 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6942 (pt)
REVERT: C  315 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6876 (mp0)
REVERT: C  326 LYS cc_start: 0.8106 (tptp) cc_final: 0.7777 (tptp)
REVERT: C  382 SER cc_start: 0.7767 (t) cc_final: 0.7404 (p)
REVERT: C  383 ARG cc_start: 0.6040 (mmm160) cc_final: 0.5772 (mmp-170)
REVERT: C  395 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6905 (ttpt)
REVERT: C  430 ARG cc_start: 0.6295 (ttm170) cc_final: 0.5481 (ttm170)
REVERT: C  438 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7539 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7973 (mmmt)
REVERT: D   64 MET cc_start: 0.7342 (mtp) cc_final: 0.7080 (mtp)
REVERT: D   83 GLU cc_start: 0.7671 (tp30) cc_final: 0.7279 (tp30)
REVERT: D   88 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7417 (tppt)
REVERT: D  107 GLN cc_start: 0.8369 (tp40) cc_final: 0.8141 (tp40)
REVERT: D  149 ASP cc_start: 0.7178 (t0) cc_final: 0.6903 (t0)
REVERT: D  152 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6766 (p)
REVERT: D  163 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7425 (mm-40)
REVERT: D  167 ASP cc_start: 0.7558 (m-30) cc_final: 0.7205 (m-30)
REVERT: D  203 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6707 (mp0)
REVERT: D  219 MET cc_start: 0.6786 (tmm) cc_final: 0.6408 (tmm)
REVERT: D  223 LYS cc_start: 0.8093 (tmtt) cc_final: 0.7701 (tmtt)
REVERT: D  236 LYS cc_start: 0.8104 (tmmt) cc_final: 0.7690 (pttp)
REVERT: D  267 GLU cc_start: 0.7740 (tp30) cc_final: 0.7134 (tp30)
REVERT: D  323 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6610 (tm-30)
REVERT: D  367 LYS cc_start: 0.8240 (tptt) cc_final: 0.7658 (tptt)
REVERT: D  381 ASN cc_start: 0.7367 (t0) cc_final: 0.7102 (t0)
REVERT: D  416 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6433 (mmm)
REVERT: D  434 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7148 (tm-30)
REVERT: D  442 THR cc_start: 0.6932 (OUTLIER) cc_final: 0.6398 (t)
REVERT: D  457 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7946 (mmmt)
REVERT: K   27 TYR cc_start: 0.8451 (m-10) cc_final: 0.8216 (m-10)
REVERT: K  105 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7959 (mp)
REVERT: K  125 VAL cc_start: 0.7430 (t) cc_final: 0.7120 (p)
REVERT: K  129 GLN cc_start: 0.7634 (tp40) cc_final: 0.7376 (tp40)
REVERT: K  154 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6738 (p0)
REVERT: L   86 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7503 (mtp)
REVERT: L  122 GLU cc_start: 0.6993 (pm20) cc_final: 0.6664 (pm20)
REVERT: L  157 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6478 (ttp80)
REVERT: L  169 GLU cc_start: 0.7396 (pp20) cc_final: 0.7145 (pp20)
  outliers start: 79
  outliers final: 50
  residues processed: 387
  average time/residue: 0.2686
  time to fit residues: 135.7730
Evaluate side-chains
  410 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 348
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  121 ASP
Chi-restraints excluded: chain C residue  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  308 ASN
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  355 PHE
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  395 LYS
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  254 LYS
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  301 LYS
Chi-restraints excluded: chain D residue  305 ARG
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  454 MET
Chi-restraints excluded: chain D residue  471 GLU
Chi-restraints excluded: chain D residue  477 MET
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  105 LEU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  154 ASP
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   86 MET
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  136 ILE
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain L residue  157 ARG
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.139219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.124867 restraints weight = 18478.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.128479 restraints weight = 9038.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.130777 restraints weight = 5203.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10067  Z= 0.219
  Angle     :  0.695  18.620  13507  Z= 0.370
  Chirality :  0.043   0.299   1515
  Planarity :  0.003   0.040   1726
  Dihedral  :  4.661  55.770   1321
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 31.03 %
    Favored  : 61.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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:  0.76 (0.26), residues: 1173
  helix:  1.07 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.06 (0.40), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP L 146 
 HIS   0.005   0.001   HIS C 112 
 PHE   0.026   0.002   PHE C 377 
 TYR   0.024   0.002   TYR D  62 
 ARG   0.005   0.000   ARG C  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04405 (  630)
  hydrogen bonds       : angle       4.56583 ( 1878)
  covalent geometry    : bond        0.00466 (10067)
  covalent geometry    : angle       0.69476 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  431 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 352
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7639 (mm-30)
REVERT: C   78 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7705 (ttm-80)
REVERT: C   83 GLU cc_start: 0.7674 (tp30) cc_final: 0.7056 (tp30)
REVERT: C  124 MET cc_start: 0.6871 (tmm) cc_final: 0.6431 (tmm)
REVERT: C  125 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7670 (t80)
REVERT: C  159 ASP cc_start: 0.7431 (t70) cc_final: 0.7015 (t0)
REVERT: C  173 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7934 (mtt180)
REVERT: C  183 ILE cc_start: 0.8573 (pt) cc_final: 0.8308 (tt)
REVERT: C  218 GLN cc_start: 0.7705 (pp30) cc_final: 0.7453 (pp30)
REVERT: C  262 LYS cc_start: 0.7696 (mmtm) cc_final: 0.7440 (mmtm)
REVERT: C  269 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6960 (pt)
REVERT: C  315 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6832 (mp0)
REVERT: C  326 LYS cc_start: 0.8092 (tptp) cc_final: 0.7770 (tptp)
REVERT: C  382 SER cc_start: 0.7887 (t) cc_final: 0.7600 (p)
REVERT: C  383 ARG cc_start: 0.5962 (mmm160) cc_final: 0.5677 (mmp-170)
REVERT: C  395 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6945 (ttpt)
REVERT: C  430 ARG cc_start: 0.6298 (ttm170) cc_final: 0.5446 (ttm170)
REVERT: C  438 ARG cc_start: 0.7764 (mmt90) cc_final: 0.7477 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7955 (mmmt)
REVERT: D   64 MET cc_start: 0.7341 (mtp) cc_final: 0.7096 (mtp)
REVERT: D   83 GLU cc_start: 0.7651 (tp30) cc_final: 0.7237 (tp30)
REVERT: D   88 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7439 (tppt)
REVERT: D  107 GLN cc_start: 0.8356 (tp40) cc_final: 0.8115 (tp40)
REVERT: D  149 ASP cc_start: 0.7202 (t0) cc_final: 0.6815 (t0)
REVERT: D  153 ARG cc_start: 0.8387 (mtt90) cc_final: 0.8165 (mtp85)
REVERT: D  162 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8498 (ttp80)
REVERT: D  163 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7390 (mm-40)
REVERT: D  167 ASP cc_start: 0.7554 (m-30) cc_final: 0.7183 (m-30)
REVERT: D  219 MET cc_start: 0.6776 (tmm) cc_final: 0.6384 (tmm)
REVERT: D  223 LYS cc_start: 0.8059 (tmtt) cc_final: 0.7717 (tmtt)
REVERT: D  236 LYS cc_start: 0.8191 (tmmt) cc_final: 0.7702 (pttp)
REVERT: D  262 LYS cc_start: 0.7320 (mmtm) cc_final: 0.7055 (mmtm)
REVERT: D  267 GLU cc_start: 0.7755 (tp30) cc_final: 0.7145 (tp30)
REVERT: D  323 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6570 (tm-30)
REVERT: D  367 LYS cc_start: 0.8239 (tptt) cc_final: 0.7680 (tptt)
REVERT: D  416 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6432 (mmm)
REVERT: D  434 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7176 (tm-30)
REVERT: D  442 THR cc_start: 0.6921 (OUTLIER) cc_final: 0.6345 (t)
REVERT: D  457 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7966 (mmmt)
REVERT: K   27 TYR cc_start: 0.8438 (m-10) cc_final: 0.8231 (m-10)
REVERT: K  129 GLN cc_start: 0.7757 (tp40) cc_final: 0.7065 (tp40)
REVERT: L   38 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7490 (mtm-85)
REVERT: L  122 GLU cc_start: 0.6963 (pm20) cc_final: 0.6642 (pm20)
REVERT: L  157 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6469 (ttp80)
REVERT: L  169 GLU cc_start: 0.7383 (pp20) cc_final: 0.7104 (pp20)
  outliers start: 79
  outliers final: 54
  residues processed: 382
  average time/residue: 0.2733
  time to fit residues: 135.1330
Evaluate side-chains
  408 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 346
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  308 ASN
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  352 PHE
Chi-restraints excluded: chain C residue  355 PHE
Chi-restraints excluded: chain C residue  395 LYS
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  445 SER
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  254 LYS
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  305 ARG
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  471 GLU
Chi-restraints excluded: chain D residue  477 MET
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  120 VAL
Chi-restraints excluded: chain L residue  136 ILE
Chi-restraints excluded: chain L residue  157 ARG
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 112 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 72 optimal weight:    0.4980
   chunk 109 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 119 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 406 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.139854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.125414 restraints weight = 18580.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.129049 restraints weight = 9062.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.131446 restraints weight = 5227.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10067  Z= 0.192
  Angle     :  0.681  18.146  13507  Z= 0.364
  Chirality :  0.043   0.298   1515
  Planarity :  0.003   0.046   1726
  Dihedral  :  4.618  56.690   1321
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 31.12 %
    Favored  : 62.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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:  0.86 (0.26), residues: 1173
  helix:  1.15 (0.18), residues: 872
  sheet:  None (None), residues: 0
  loop : -1.03 (0.40), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP L 146 
 HIS   0.004   0.001   HIS C 112 
 PHE   0.029   0.002   PHE C  21 
 TYR   0.023   0.002   TYR D  62 
 ARG   0.007   0.000   ARG D  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  630)
  hydrogen bonds       : angle       4.51737 ( 1878)
  covalent geometry    : bond        0.00413 (10067)
  covalent geometry    : angle       0.68086 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  424 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 350
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7641 (mm-30)
REVERT: C   78 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7700 (ttm-80)
REVERT: C   83 GLU cc_start: 0.7703 (tp30) cc_final: 0.7086 (tp30)
REVERT: C  124 MET cc_start: 0.6826 (tmm) cc_final: 0.6523 (tmm)
REVERT: C  125 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7752 (t80)
REVERT: C  159 ASP cc_start: 0.7431 (t70) cc_final: 0.6942 (t0)
REVERT: C  173 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7684 (mtt180)
REVERT: C  218 GLN cc_start: 0.7699 (pp30) cc_final: 0.7403 (pp30)
REVERT: C  223 LYS cc_start: 0.7811 (tptp) cc_final: 0.7376 (ttpp)
REVERT: C  236 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7550 (tmmt)
REVERT: C  262 LYS cc_start: 0.7711 (mmtm) cc_final: 0.7456 (mmtm)
REVERT: C  315 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6822 (mp0)
REVERT: C  326 LYS cc_start: 0.8072 (tptp) cc_final: 0.7823 (tptp)
REVERT: C  330 SER cc_start: 0.8468 (m) cc_final: 0.8066 (p)
REVERT: C  381 ASN cc_start: 0.7063 (t0) cc_final: 0.6592 (t0)
REVERT: C  382 SER cc_start: 0.7961 (t) cc_final: 0.7572 (p)
REVERT: C  395 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6933 (ttpt)
REVERT: C  430 ARG cc_start: 0.6313 (ttm170) cc_final: 0.5722 (ttm170)
REVERT: C  438 ARG cc_start: 0.7751 (mmt90) cc_final: 0.7472 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7978 (mmmt)
REVERT: D   83 GLU cc_start: 0.7663 (tp30) cc_final: 0.7210 (tp30)
REVERT: D   88 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7431 (tppt)
REVERT: D  149 ASP cc_start: 0.7224 (t0) cc_final: 0.6893 (t0)
REVERT: D  152 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6669 (p)
REVERT: D  162 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8485 (ttp80)
REVERT: D  163 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7286 (mm-40)
REVERT: D  167 ASP cc_start: 0.7547 (m-30) cc_final: 0.7167 (m-30)
REVERT: D  219 MET cc_start: 0.6782 (tmm) cc_final: 0.6377 (tmm)
REVERT: D  223 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7703 (tmtt)
REVERT: D  236 LYS cc_start: 0.8214 (tmmt) cc_final: 0.7727 (pttp)
REVERT: D  262 LYS cc_start: 0.7328 (mmtm) cc_final: 0.7015 (mmtm)
REVERT: D  267 GLU cc_start: 0.7766 (tp30) cc_final: 0.7153 (tp30)
REVERT: D  323 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: D  367 LYS cc_start: 0.8220 (tptt) cc_final: 0.7625 (tptt)
REVERT: D  416 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6334 (mmm)
REVERT: D  424 GLU cc_start: 0.7200 (tp30) cc_final: 0.6773 (tp30)
REVERT: D  425 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6913 (mtpt)
REVERT: D  434 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: D  442 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6282 (t)
REVERT: D  457 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7922 (mmmt)
REVERT: K   92 LEU cc_start: 0.7641 (mm) cc_final: 0.7399 (mp)
REVERT: K  129 GLN cc_start: 0.7735 (tp40) cc_final: 0.7288 (tp40)
REVERT: K  154 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6773 (p0)
REVERT: K  169 GLU cc_start: 0.7521 (pp20) cc_final: 0.7242 (pp20)
REVERT: L  154 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6830 (p0)
  outliers start: 74
  outliers final: 53
  residues processed: 375
  average time/residue: 0.2680
  time to fit residues: 130.8909
Evaluate side-chains
  401 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 338
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  236 LYS
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  308 ASN
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain C residue  352 PHE
Chi-restraints excluded: chain C residue  355 PHE
Chi-restraints excluded: chain C residue  395 LYS
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  254 LYS
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  305 ARG
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  454 MET
Chi-restraints excluded: chain D residue  471 GLU
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  154 ASP
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain L residue  120 VAL
Chi-restraints excluded: chain L residue  154 ASP
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 118 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0970
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 42 optimal weight:    0.7980
   chunk 112 optimal weight:    0.3980
   overall best weight:    0.4378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.140228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.125739 restraints weight = 18693.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.129372 restraints weight = 9152.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.131747 restraints weight = 5285.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10067  Z= 0.173
  Angle     :  0.692  18.070  13507  Z= 0.365
  Chirality :  0.042   0.287   1515
  Planarity :  0.003   0.042   1726
  Dihedral  :  4.560  56.756   1321
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 31.74 %
    Favored  : 61.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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:  0.95 (0.26), residues: 1173
  helix:  1.24 (0.18), residues: 872
  sheet:  None (None), residues: 0
  loop : -1.07 (0.40), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP L 146 
 HIS   0.003   0.001   HIS D 112 
 PHE   0.033   0.002   PHE D 377 
 TYR   0.039   0.002   TYR D  62 
 ARG   0.008   0.000   ARG D 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (  630)
  hydrogen bonds       : angle       4.47530 ( 1878)
  covalent geometry    : bond        0.00379 (10067)
  covalent geometry    : angle       0.69231 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  424 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 348
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7636 (mm-30)
REVERT: C   78 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7691 (ttm-80)
REVERT: C   83 GLU cc_start: 0.7691 (tp30) cc_final: 0.7078 (tp30)
REVERT: C  124 MET cc_start: 0.6785 (tmm) cc_final: 0.6491 (tmm)
REVERT: C  125 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7701 (t80)
REVERT: C  159 ASP cc_start: 0.7379 (t70) cc_final: 0.6498 (t0)
REVERT: C  163 GLN cc_start: 0.7375 (mp10) cc_final: 0.6254 (mp10)
REVERT: C  173 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7687 (mtt90)
REVERT: C  218 GLN cc_start: 0.7710 (pp30) cc_final: 0.7448 (pp30)
REVERT: C  223 LYS cc_start: 0.7788 (tptp) cc_final: 0.7383 (ttpp)
REVERT: C  262 LYS cc_start: 0.7670 (mmtm) cc_final: 0.7361 (mmtm)
REVERT: C  315 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6848 (mp0)
REVERT: C  326 LYS cc_start: 0.8056 (tptp) cc_final: 0.7802 (tptp)
REVERT: C  330 SER cc_start: 0.8503 (m) cc_final: 0.8036 (p)
REVERT: C  381 ASN cc_start: 0.7013 (t0) cc_final: 0.6519 (t0)
REVERT: C  382 SER cc_start: 0.7931 (t) cc_final: 0.7591 (p)
REVERT: C  395 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6945 (ttpt)
REVERT: C  430 ARG cc_start: 0.6336 (ttm170) cc_final: 0.5710 (ttm170)
REVERT: C  438 ARG cc_start: 0.7732 (mmt90) cc_final: 0.7503 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8309 (mmmt) cc_final: 0.7957 (mmmt)
REVERT: D   78 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7735 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7626 (tp30) cc_final: 0.7146 (tp30)
REVERT: D   88 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7400 (tppt)
REVERT: D  149 ASP cc_start: 0.7257 (t0) cc_final: 0.6822 (t0)
REVERT: D  162 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8459 (ttp80)
REVERT: D  163 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7319 (mm-40)
REVERT: D  167 ASP cc_start: 0.7531 (m-30) cc_final: 0.7163 (m-30)
REVERT: D  219 MET cc_start: 0.6760 (tmm) cc_final: 0.6326 (tmm)
REVERT: D  223 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7681 (tmtt)
REVERT: D  236 LYS cc_start: 0.8226 (tmmt) cc_final: 0.7750 (pttp)
REVERT: D  262 LYS cc_start: 0.7288 (mmtm) cc_final: 0.7024 (mmtm)
REVERT: D  267 GLU cc_start: 0.7753 (tp30) cc_final: 0.7173 (tp30)
REVERT: D  315 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6932 (mm-30)
REVERT: D  323 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6451 (tm-30)
REVERT: D  367 LYS cc_start: 0.8225 (tptt) cc_final: 0.7652 (tptt)
REVERT: D  416 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6349 (mmm)
REVERT: D  434 GLN cc_start: 0.7462 (tm-30) cc_final: 0.6550 (tm-30)
REVERT: D  438 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7369 (mmt90)
REVERT: D  442 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.6278 (t)
REVERT: D  457 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7921 (mmmt)
REVERT: K  105 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7965 (mp)
REVERT: K  125 VAL cc_start: 0.7391 (t) cc_final: 0.7160 (p)
REVERT: K  129 GLN cc_start: 0.7724 (tp40) cc_final: 0.7150 (tp40)
REVERT: K  154 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6677 (p0)
REVERT: L  154 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6841 (p0)
REVERT: L  169 GLU cc_start: 0.7421 (pp20) cc_final: 0.7124 (pp20)
  outliers start: 76
  outliers final: 52
  residues processed: 378
  average time/residue: 0.2769
  time to fit residues: 139.1917
Evaluate side-chains
  404 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 343
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  183 ILE
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  308 ASN
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain C residue  352 PHE
Chi-restraints excluded: chain C residue  355 PHE
Chi-restraints excluded: chain C residue  395 LYS
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   62 TYR
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  254 LYS
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  454 MET
Chi-restraints excluded: chain D residue  471 GLU
Chi-restraints excluded: chain D residue  477 MET
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue  105 LEU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  154 ASP
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  136 ILE
Chi-restraints excluded: chain L residue  154 ASP
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 73 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0470
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 11 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0670
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.3216

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

Flipped N/Q/H residues before XYZ refinement:
D 250 HIS
D 406 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.141323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.127016 restraints weight = 18735.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.130665 restraints weight = 9124.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.133013 restraints weight = 5238.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10067  Z= 0.152
  Angle     :  0.701  17.632  13507  Z= 0.364
  Chirality :  0.041   0.288   1515
  Planarity :  0.004   0.039   1726
  Dihedral  :  4.507  56.402   1321
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 32.73 %
    Favored  : 61.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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 (0.26), residues: 1173
  helix:  1.33 (0.18), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.08 (0.39), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L 146 
 HIS   0.005   0.001   HIS L  32 
 PHE   0.032   0.002   PHE D 377 
 TYR   0.027   0.002   TYR D  62 
 ARG   0.010   0.001   ARG C 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  630)
  hydrogen bonds       : angle       4.43103 ( 1878)
  covalent geometry    : bond        0.00335 (10067)
  covalent geometry    : angle       0.70082 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 341
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7612 (mm-30)
REVERT: C   83 GLU cc_start: 0.7677 (tp30) cc_final: 0.7072 (tp30)
REVERT: C  124 MET cc_start: 0.6753 (tmm) cc_final: 0.6463 (tmm)
REVERT: C  125 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7635 (t80)
REVERT: C  159 ASP cc_start: 0.7371 (t70) cc_final: 0.6495 (t0)
REVERT: C  163 GLN cc_start: 0.7372 (mp10) cc_final: 0.6224 (mp10)
REVERT: C  173 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7689 (mtt180)
REVERT: C  218 GLN cc_start: 0.7680 (pp30) cc_final: 0.7357 (pp30)
REVERT: C  219 MET cc_start: 0.6952 (mmm) cc_final: 0.6635 (mmm)
REVERT: C  262 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7369 (mmtm)
REVERT: C  315 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6789 (mp0)
REVERT: C  326 LYS cc_start: 0.8041 (tptp) cc_final: 0.7607 (tptp)
REVERT: C  330 SER cc_start: 0.8476 (m) cc_final: 0.7949 (m)
REVERT: C  381 ASN cc_start: 0.7007 (t0) cc_final: 0.6503 (t0)
REVERT: C  382 SER cc_start: 0.7986 (t) cc_final: 0.7664 (p)
REVERT: C  395 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6940 (ttpt)
REVERT: C  430 ARG cc_start: 0.6240 (ttm170) cc_final: 0.5532 (ttm170)
REVERT: C  438 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7363 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7975 (mmmt)
REVERT: D   83 GLU cc_start: 0.7606 (tp30) cc_final: 0.7113 (tp30)
REVERT: D   88 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7399 (tppt)
REVERT: D  128 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7300 (mmm-85)
REVERT: D  149 ASP cc_start: 0.7251 (t0) cc_final: 0.6818 (t0)
REVERT: D  163 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7270 (mm-40)
REVERT: D  167 ASP cc_start: 0.7530 (m-30) cc_final: 0.7161 (m-30)
REVERT: D  219 MET cc_start: 0.6740 (tmm) cc_final: 0.6314 (tmm)
REVERT: D  223 LYS cc_start: 0.7998 (tmtt) cc_final: 0.7703 (tmtt)
REVERT: D  236 LYS cc_start: 0.8223 (tmmt) cc_final: 0.7742 (pttp)
REVERT: D  262 LYS cc_start: 0.7311 (mmtm) cc_final: 0.7032 (mmtm)
REVERT: D  267 GLU cc_start: 0.7722 (tp30) cc_final: 0.7161 (tp30)
REVERT: D  288 LEU cc_start: 0.8333 (pt) cc_final: 0.8005 (pp)
REVERT: D  315 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6870 (mm-30)
REVERT: D  323 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6395 (tm-30)
REVERT: D  367 LYS cc_start: 0.8210 (tptt) cc_final: 0.7651 (tptt)
REVERT: D  416 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6308 (mmm)
REVERT: D  434 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7167 (tm-30)
REVERT: D  457 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7887 (mmmt)
REVERT: K   78 MET cc_start: 0.7745 (ttm) cc_final: 0.6318 (tpp)
REVERT: K   85 GLU cc_start: 0.7666 (tt0) cc_final: 0.6364 (tt0)
REVERT: K  125 VAL cc_start: 0.7393 (t) cc_final: 0.7112 (p)
REVERT: K  129 GLN cc_start: 0.7698 (tp40) cc_final: 0.7115 (tp40)
REVERT: K  154 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6695 (p0)
REVERT: L   38 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7396 (mtm-85)
REVERT: L   92 LEU cc_start: 0.7850 (mt) cc_final: 0.7643 (mt)
  outliers start: 66
  outliers final: 54
  residues processed: 365
  average time/residue: 0.2667
  time to fit residues: 126.8246
Evaluate side-chains
  387 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 327
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  183 ILE
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain C residue  352 PHE
Chi-restraints excluded: chain C residue  355 PHE
Chi-restraints excluded: chain C residue  395 LYS
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  254 LYS
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  317 MET
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  352 PHE
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  471 GLU
Chi-restraints excluded: chain D residue  477 MET
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  154 ASP
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   37 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  136 ILE
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 107 optimal weight:    0.2980
   chunk 105 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9980
   chunk 84 optimal weight:    0.3980
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 286 HIS
D 286 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.141559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.127279 restraints weight = 18552.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.130912 restraints weight = 9059.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.133193 restraints weight = 5214.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10067  Z= 0.192
  Angle     :  0.732  17.878  13507  Z= 0.384
  Chirality :  0.043   0.289   1515
  Planarity :  0.004   0.050   1726
  Dihedral  :  4.589  57.121   1321
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 32.10 %
    Favored  : 62.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    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:  0.97 (0.26), residues: 1173
  helix:  1.25 (0.18), residues: 881
  sheet:  None (None), residues: 0
  loop : -1.12 (0.40), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 146 
 HIS   0.004   0.001   HIS L  32 
 PHE   0.033   0.002   PHE C 377 
 TYR   0.031   0.002   TYR D  62 
 ARG   0.007   0.001   ARG C 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  630)
  hydrogen bonds       : angle       4.49521 ( 1878)
  covalent geometry    : bond        0.00420 (10067)
  covalent geometry    : angle       0.73235 (13507)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 337
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7641 (mm-30)
REVERT: C   62 TYR cc_start: 0.6809 (t80) cc_final: 0.6161 (t80)
REVERT: C   78 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7696 (ttm-80)
REVERT: C   83 GLU cc_start: 0.7699 (tp30) cc_final: 0.7085 (tp30)
REVERT: C  124 MET cc_start: 0.6816 (tmm) cc_final: 0.6492 (tmm)
REVERT: C  125 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7658 (t80)
REVERT: C  159 ASP cc_start: 0.7350 (t70) cc_final: 0.6507 (t0)
REVERT: C  163 GLN cc_start: 0.7372 (mp10) cc_final: 0.6259 (mp10)
REVERT: C  173 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7659 (mtt90)
REVERT: C  218 GLN cc_start: 0.7694 (pp30) cc_final: 0.7381 (pp30)
REVERT: C  219 MET cc_start: 0.6997 (mmm) cc_final: 0.6706 (mmm)
REVERT: C  262 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7374 (mmtm)
REVERT: C  315 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6816 (mp0)
REVERT: C  326 LYS cc_start: 0.8070 (tptp) cc_final: 0.7816 (tptp)
REVERT: C  330 SER cc_start: 0.8488 (m) cc_final: 0.7983 (p)
REVERT: C  381 ASN cc_start: 0.7092 (t0) cc_final: 0.6624 (t0)
REVERT: C  382 SER cc_start: 0.7986 (t) cc_final: 0.7592 (p)
REVERT: C  395 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6912 (ttpt)
REVERT: C  430 ARG cc_start: 0.6273 (ttm170) cc_final: 0.5567 (ttm170)
REVERT: C  438 ARG cc_start: 0.7683 (mmt90) cc_final: 0.7434 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7975 (mmmt)
REVERT: D   78 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7761 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7601 (tp30) cc_final: 0.7092 (tp30)
REVERT: D   88 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7397 (tppt)
REVERT: D  149 ASP cc_start: 0.7247 (t0) cc_final: 0.6810 (t0)
REVERT: D  162 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8338 (ttp80)
REVERT: D  163 GLN cc_start: 0.7917 (mm-40) cc_final: 0.6585 (mp10)
REVERT: D  167 ASP cc_start: 0.7535 (m-30) cc_final: 0.7186 (m-30)
REVERT: D  223 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7703 (tmtt)
REVERT: D  236 LYS cc_start: 0.8264 (tmmt) cc_final: 0.7968 (ttpp)
REVERT: D  262 LYS cc_start: 0.7301 (mmtm) cc_final: 0.7016 (mmtm)
REVERT: D  267 GLU cc_start: 0.7738 (tp30) cc_final: 0.7175 (tp30)
REVERT: D  315 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6948 (mm-30)
REVERT: D  323 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6449 (tm-30)
REVERT: D  367 LYS cc_start: 0.8237 (tptt) cc_final: 0.7651 (tptt)
REVERT: D  416 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6355 (mmm)
REVERT: D  442 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6215 (t)
REVERT: D  457 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7901 (mmmt)
REVERT: K   78 MET cc_start: 0.7776 (ttm) cc_final: 0.6176 (tpp)
REVERT: K   85 GLU cc_start: 0.7834 (tt0) cc_final: 0.6400 (tt0)
REVERT: K  125 VAL cc_start: 0.7492 (t) cc_final: 0.7200 (p)
REVERT: K  129 GLN cc_start: 0.7712 (tp40) cc_final: 0.7014 (tp40)
REVERT: K  154 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6726 (p0)
REVERT: L   38 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7453 (mtm-85)
REVERT: L   92 LEU cc_start: 0.7872 (mt) cc_final: 0.7660 (mt)
REVERT: L  154 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6857 (p0)
  outliers start: 62
  outliers final: 46
  residues processed: 357
  average time/residue: 0.2651
  time to fit residues: 124.1914
Evaluate side-chains
  386 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 332
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  282 SER
Chi-restraints excluded: chain C residue  315 GLU
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain C residue  352 PHE
Chi-restraints excluded: chain C residue  355 PHE
Chi-restraints excluded: chain C residue  395 LYS
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
Chi-restraints excluded: chain D residue   88 LYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  257 GLU
Chi-restraints excluded: chain D residue  287 MET
Chi-restraints excluded: chain D residue  305 ARG
Chi-restraints excluded: chain D residue  308 ASN
Chi-restraints excluded: chain D residue  317 MET
Chi-restraints excluded: chain D residue  345 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  416 MET
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  471 GLU
Chi-restraints excluded: chain D residue  477 MET
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   87 GLU
Chi-restraints excluded: chain K residue  136 ILE
Chi-restraints excluded: chain K residue  154 ASP
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain K residue  158 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  136 ILE
Chi-restraints excluded: chain L residue  154 ASP
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain L residue  158 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0010
   chunk 6 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
C 188 GLN
D 381 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.139391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.125065 restraints weight = 18670.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.128705 restraints weight = 9113.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.131016 restraints weight = 5243.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10067  Z= 0.196
  Angle     :  0.750  17.875  13507  Z= 0.390
  Chirality :  0.044   0.286   1515
  Planarity :  0.004   0.060   1726
  Dihedral  :  4.637  56.951   1321
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 33.00 %
    Favored  : 61.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1173
  helix:  1.21 (0.18), residues: 877
  sheet:  None (None), residues: 0
  loop : -1.09 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP L 146 
 HIS   0.004   0.001   HIS C 112 
 PHE   0.036   0.002   PHE C 224 
 TYR   0.032   0.002   TYR D  62 
 ARG   0.010   0.001   ARG C 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  630)
  hydrogen bonds       : angle       4.53344 ( 1878)
  covalent geometry    : bond        0.00429 (10067)
  covalent geometry    : angle       0.74994 (13507)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4151.40 seconds
wall clock time: 73 minutes 25.36 seconds (4405.36 seconds total)