Starting phenix.real_space_refine
on Fri Oct 10 23:42:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k8t_36961/10_2025/8k8t_36961.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k8t_36961/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k8t_36961/10_2025/8k8t_36961.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k8t_36961/10_2025/8k8t_36961.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k8t_36961/10_2025/8k8t_36961.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k8t_36961/10_2025/8k8t_36961.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.79, per 1000 atoms: 0.28
  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: 1.00
  Conformation dependent library (CDL) restraints added in 296.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.32
  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: 1.47

  Time building geometry restraints manager: 1.28 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:             12.660
  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:          0.280
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.030
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.530
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (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
 ARG   0.005   0.001   ARG D  78 
 TYR   0.018   0.002   TYR D 320 
 PHE   0.038   0.002   PHE C 224 
 TRP   0.010   0.002   TRP D  34 
 HIS   0.005   0.001   HIS C 250 

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

*********************** 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  : 0.497 
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: 0.7816 (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: 0.8298 (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: 0.7121 (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: 0.7741 (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: 0.1210
  time to fit residues: 59.5335
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  : 0.376 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0980
   chunk 117 optimal weight:    0.0970
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
C 188 GLN
** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 435 HIS
D  60 ASN
D 106 ASN
D 218 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.144009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.129779 restraints weight = 18969.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.133500 restraints weight = 9146.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.135818 restraints weight = 5206.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.137289 restraints weight = 3344.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.138303 restraints weight = 2388.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10067  Z= 0.166
  Angle     :  0.670  20.900  13507  Z= 0.358
  Chirality :  0.041   0.309   1515
  Planarity :  0.004   0.039   1726
  Dihedral  :  5.752  72.345   1346
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.26 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 25.09 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.26), residues: 1173
  helix:  1.09 (0.18), residues: 877
  sheet:  None (None), residues: 0
  loop : -0.92 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  90 
 TYR   0.017   0.002   TYR D  29 
 PHE   0.026   0.002   PHE C 377 
 TRP   0.005   0.001   TRP K 146 
 HIS   0.003   0.001   HIS D 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10067)
  covalent geometry    : angle       0.67035 (13507)
  hydrogen bonds       : bond        0.04490 (  630)
  hydrogen bonds       : angle       4.79860 ( 1878)

*********************** 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: 65
    poor density    : 339
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7550 (mm-30)
REVERT: C   64 MET cc_start: 0.7994 (tpp) cc_final: 0.7693 (tpp)
REVERT: C   72 LYS cc_start: 0.8477 (tptm) cc_final: 0.8252 (tptm)
REVERT: C   83 GLU cc_start: 0.7665 (tp30) cc_final: 0.7145 (tp30)
REVERT: C  163 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6555 (mp10)
REVERT: C  191 MET cc_start: 0.7959 (mtt) cc_final: 0.7727 (mtt)
REVERT: C  224 PHE cc_start: 0.6960 (m-80) cc_final: 0.6735 (m-80)
REVERT: C  243 GLU cc_start: 0.7589 (tp30) cc_final: 0.7268 (tp30)
REVERT: C  258 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7131 (mm-30)
REVERT: C  262 LYS cc_start: 0.7426 (mmtm) cc_final: 0.6849 (mmtm)
REVERT: C  300 TYR cc_start: 0.7872 (t80) cc_final: 0.7670 (t80)
REVERT: C  315 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6934 (mp0)
REVERT: C  326 LYS cc_start: 0.8078 (tptp) cc_final: 0.7668 (tptp)
REVERT: C  434 GLN cc_start: 0.7557 (tp40) cc_final: 0.7333 (tp40)
REVERT: C  438 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7510 (mmt90)
REVERT: D   47 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7935 (mmmt)
REVERT: D   62 TYR cc_start: 0.6592 (t80) cc_final: 0.6347 (t80)
REVERT: D   64 MET cc_start: 0.7077 (mtp) cc_final: 0.6770 (mtp)
REVERT: D   78 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7759 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7583 (tp30) cc_final: 0.7289 (tp30)
REVERT: D  128 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7589 (mmm-85)
REVERT: D  167 ASP cc_start: 0.7454 (m-30) cc_final: 0.7174 (m-30)
REVERT: D  203 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6556 (mp0)
REVERT: D  267 GLU cc_start: 0.7689 (tp30) cc_final: 0.7150 (tp30)
REVERT: D  315 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7069 (mm-30)
REVERT: D  416 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6195 (mmm)
REVERT: D  424 GLU cc_start: 0.7450 (mp0) cc_final: 0.7227 (tp30)
REVERT: D  438 ARG cc_start: 0.7868 (mmt90) cc_final: 0.7360 (mmt90)
REVERT: D  442 THR cc_start: 0.6883 (OUTLIER) cc_final: 0.6364 (t)
REVERT: K   27 TYR cc_start: 0.8321 (m-10) cc_final: 0.8050 (m-10)
REVERT: K   92 LEU cc_start: 0.7708 (mm) cc_final: 0.7491 (mt)
REVERT: L   38 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7478 (mtm-85)
REVERT: L   73 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.6421 (p0)
REVERT: L  122 GLU cc_start: 0.6905 (pm20) cc_final: 0.6640 (pm20)
REVERT: L  169 GLU cc_start: 0.7308 (pp20) cc_final: 0.7031 (pp20)
  outliers start: 65
  outliers final: 29
  residues processed: 370
  average time/residue: 0.1094
  time to fit residues: 54.5995
Evaluate side-chains
  362 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 328
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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   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 80 optimal weight:    0.0770
   chunk 106 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
C 163 GLN
D 106 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.140441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.126069 restraints weight = 18757.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.129746 restraints weight = 9055.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.132106 restraints weight = 5186.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.133492 restraints weight = 3341.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.134509 restraints weight = 2426.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10067  Z= 0.214
  Angle     :  0.667  18.838  13507  Z= 0.359
  Chirality :  0.043   0.313   1515
  Planarity :  0.003   0.035   1726
  Dihedral  :  4.848  50.054   1329
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.69 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 28.06 %
    Favored  : 65.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.26), residues: 1173
  helix:  1.08 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.00 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  59 
 TYR   0.017   0.002   TYR D  29 
 PHE   0.019   0.002   PHE C 391 
 TRP   0.016   0.002   TRP L 146 
 HIS   0.005   0.001   HIS D 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10067)
  covalent geometry    : angle       0.66679 (13507)
  hydrogen bonds       : bond        0.04591 (  630)
  hydrogen bonds       : angle       4.65460 ( 1878)

*********************** 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
  412 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 345
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7646 (mm-30)
REVERT: C   83 GLU cc_start: 0.7691 (tp30) cc_final: 0.7080 (tp30)
REVERT: C  124 MET cc_start: 0.6757 (tmm) cc_final: 0.6512 (tmm)
REVERT: C  125 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7788 (t80)
REVERT: C  147 PHE cc_start: 0.7846 (t80) cc_final: 0.7394 (t80)
REVERT: C  173 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7937 (mtt180)
REVERT: C  213 SER cc_start: 0.8498 (t) cc_final: 0.8075 (p)
REVERT: C  218 GLN cc_start: 0.7702 (pp30) cc_final: 0.7331 (pp30)
REVERT: C  258 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7188 (mm-30)
REVERT: C  262 LYS cc_start: 0.7487 (mmtm) cc_final: 0.7275 (mmtm)
REVERT: C  315 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6896 (mp0)
REVERT: C  326 LYS cc_start: 0.8109 (tptp) cc_final: 0.7721 (tptp)
REVERT: C  438 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7522 (mmm-85)
REVERT: D   52 LEU cc_start: 0.8530 (mt) cc_final: 0.8274 (mt)
REVERT: D   64 MET cc_start: 0.7394 (mtp) cc_final: 0.7081 (mtp)
REVERT: D   78 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7763 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7612 (tp30) cc_final: 0.7289 (tp30)
REVERT: D   88 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7297 (tppt)
REVERT: D  107 GLN cc_start: 0.8447 (tp40) cc_final: 0.8222 (tp40)
REVERT: D  124 MET cc_start: 0.6608 (tmm) cc_final: 0.6386 (tmm)
REVERT: D  125 TYR cc_start: 0.8024 (t80) cc_final: 0.7668 (t80)
REVERT: D  128 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7579 (mmm-85)
REVERT: D  163 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7500 (mm-40)
REVERT: D  167 ASP cc_start: 0.7487 (m-30) cc_final: 0.7169 (m-30)
REVERT: D  223 LYS cc_start: 0.8082 (tmtt) cc_final: 0.7724 (tmtt)
REVERT: D  236 LYS cc_start: 0.7853 (tmmt) cc_final: 0.7557 (tmmt)
REVERT: D  267 GLU cc_start: 0.7683 (tp30) cc_final: 0.7162 (tp30)
REVERT: D  299 MET cc_start: 0.7482 (tmm) cc_final: 0.7220 (tmm)
REVERT: D  315 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7074 (mm-30)
REVERT: D  323 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6664 (tm-30)
REVERT: D  367 LYS cc_start: 0.8223 (tptt) cc_final: 0.7760 (tptt)
REVERT: D  416 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6212 (mmm)
REVERT: D  434 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7171 (tm-30)
REVERT: D  442 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6365 (t)
REVERT: D  457 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7962 (mmmt)
REVERT: K   27 TYR cc_start: 0.8363 (m-10) cc_final: 0.8151 (m-10)
REVERT: K   85 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6977 (tm-30)
REVERT: L   38 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7364 (mtm-85)
REVERT: L   84 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7408 (ttpp)
REVERT: L  122 GLU cc_start: 0.6961 (pm20) cc_final: 0.6744 (pm20)
  outliers start: 67
  outliers final: 42
  residues processed: 368
  average time/residue: 0.1129
  time to fit residues: 55.8328
Evaluate side-chains
  386 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 339
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  125 TYR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  237 VAL
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 C residue  455 ILE
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   29 TYR
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  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:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0670
   chunk 80 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0870
   chunk 67 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.4896

-------------------------------------------------------------------------------
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
C 435 HIS
D 106 ASN
D 381 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.141203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.126930 restraints weight = 19040.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.130627 restraints weight = 9160.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.132931 restraints weight = 5235.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.134213 restraints weight = 3377.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.135348 restraints weight = 2492.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10067  Z= 0.175
  Angle     :  0.632  18.497  13507  Z= 0.341
  Chirality :  0.041   0.300   1515
  Planarity :  0.003   0.027   1726
  Dihedral  :  4.536  53.450   1323
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 29.77 %
    Favored  : 64.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1173
  helix:  1.19 (0.18), residues: 875
  sheet:  None (None), residues: 0
  loop : -1.03 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  59 
 TYR   0.017   0.002   TYR D  29 
 PHE   0.026   0.002   PHE C 377 
 TRP   0.013   0.002   TRP L 146 
 HIS   0.004   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (10067)
  covalent geometry    : angle       0.63240 (13507)
  hydrogen bonds       : bond        0.04198 (  630)
  hydrogen bonds       : angle       4.50501 ( 1878)

*********************** 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
  417 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 349
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7633 (mm-30)
REVERT: C   62 TYR cc_start: 0.7072 (t80) cc_final: 0.6692 (t80)
REVERT: C   83 GLU cc_start: 0.7632 (tp30) cc_final: 0.7047 (tp30)
REVERT: C  124 MET cc_start: 0.6722 (tmm) cc_final: 0.6495 (tmm)
REVERT: C  159 ASP cc_start: 0.7337 (t70) cc_final: 0.7040 (t0)
REVERT: C  163 GLN cc_start: 0.7508 (mp-120) cc_final: 0.7019 (mp10)
REVERT: C  173 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7947 (mtt180)
REVERT: C  213 SER cc_start: 0.8355 (t) cc_final: 0.8070 (p)
REVERT: C  218 GLN cc_start: 0.7644 (pp30) cc_final: 0.7327 (pp30)
REVERT: C  262 LYS cc_start: 0.7598 (mmtm) cc_final: 0.7373 (mmtm)
REVERT: C  315 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6822 (mp0)
REVERT: C  326 LYS cc_start: 0.8098 (tptp) cc_final: 0.7720 (tptp)
REVERT: C  373 ASP cc_start: 0.6605 (m-30) cc_final: 0.6404 (m-30)
REVERT: C  438 ARG cc_start: 0.7663 (mmt90) cc_final: 0.7414 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7847 (mmmt)
REVERT: D   46 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7600 (mtm110)
REVERT: D   64 MET cc_start: 0.7383 (mtp) cc_final: 0.7151 (mtp)
REVERT: D   78 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7763 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7658 (tp30) cc_final: 0.7269 (tp30)
REVERT: D   88 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7268 (tppt)
REVERT: D  124 MET cc_start: 0.6533 (tmm) cc_final: 0.6264 (tmm)
REVERT: D  125 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7478 (t80)
REVERT: D  149 ASP cc_start: 0.7163 (t0) cc_final: 0.6928 (t0)
REVERT: D  163 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7405 (mm-40)
REVERT: D  167 ASP cc_start: 0.7497 (m-30) cc_final: 0.7149 (m-30)
REVERT: D  212 MET cc_start: 0.7579 (tmm) cc_final: 0.7272 (tmm)
REVERT: D  223 LYS cc_start: 0.8039 (tmtt) cc_final: 0.7668 (tmtt)
REVERT: D  236 LYS cc_start: 0.7953 (tmmt) cc_final: 0.7664 (pttt)
REVERT: D  247 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7571 (ttm-80)
REVERT: D  267 GLU cc_start: 0.7705 (tp30) cc_final: 0.7209 (tp30)
REVERT: D  315 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6962 (mm-30)
REVERT: D  323 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6560 (tm-30)
REVERT: D  367 LYS cc_start: 0.8204 (tptt) cc_final: 0.7651 (tptt)
REVERT: D  416 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6254 (mmm)
REVERT: D  424 GLU cc_start: 0.7250 (tp30) cc_final: 0.6772 (tp30)
REVERT: D  434 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7164 (tm-30)
REVERT: D  442 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6267 (t)
REVERT: D  457 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7873 (mmmt)
REVERT: K   27 TYR cc_start: 0.8370 (m-10) cc_final: 0.8167 (m-10)
REVERT: K   90 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6894 (mp0)
REVERT: K  101 MET cc_start: 0.8266 (mmm) cc_final: 0.8062 (tpt)
REVERT: K  104 ILE cc_start: 0.8656 (tt) cc_final: 0.8432 (tt)
REVERT: K  105 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7829 (mm)
REVERT: L   38 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7454 (mtm-85)
REVERT: L  122 GLU cc_start: 0.6953 (pm20) cc_final: 0.6657 (pm20)
REVERT: L  129 GLN cc_start: 0.8053 (mm110) cc_final: 0.7667 (tp40)
REVERT: L  169 GLU cc_start: 0.7371 (pp20) cc_final: 0.7127 (pp20)
  outliers start: 68
  outliers final: 44
  residues processed: 375
  average time/residue: 0.1240
  time to fit residues: 61.7963
Evaluate side-chains
  384 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 333
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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   85 LEU
Chi-restraints excluded: chain C residue  118 MET
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  424 GLU
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  193 LEU
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   89 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   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 96 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 51 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 79 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 101 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   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 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
D 381 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.141571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.126627 restraints weight = 18806.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.130440 restraints weight = 9089.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.132831 restraints weight = 5226.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.134358 restraints weight = 3389.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.135200 restraints weight = 2432.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10067  Z= 0.183
  Angle     :  0.641  18.164  13507  Z= 0.344
  Chirality :  0.042   0.299   1515
  Planarity :  0.003   0.041   1726
  Dihedral  :  4.549  55.164   1323
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 30.22 %
    Favored  : 63.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.26), residues: 1173
  helix:  1.21 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.02 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  90 
 TYR   0.023   0.002   TYR C 125 
 PHE   0.031   0.002   PHE D 377 
 TRP   0.024   0.002   TRP L 146 
 HIS   0.004   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (10067)
  covalent geometry    : angle       0.64143 (13507)
  hydrogen bonds       : bond        0.04187 (  630)
  hydrogen bonds       : angle       4.46415 ( 1878)

*********************** 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
  409 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 338
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7631 (mm-30)
REVERT: C   83 GLU cc_start: 0.7671 (tp30) cc_final: 0.7033 (tp30)
REVERT: C  124 MET cc_start: 0.6752 (tmm) cc_final: 0.6354 (tmm)
REVERT: C  125 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7599 (t80)
REVERT: C  159 ASP cc_start: 0.7432 (t70) cc_final: 0.6979 (t0)
REVERT: C  163 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6998 (mp10)
REVERT: C  173 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7751 (mtt180)
REVERT: C  213 SER cc_start: 0.8406 (t) cc_final: 0.8161 (p)
REVERT: C  218 GLN cc_start: 0.7699 (pp30) cc_final: 0.7378 (pp30)
REVERT: C  262 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7354 (mmtm)
REVERT: C  269 ILE cc_start: 0.7186 (pp) cc_final: 0.6883 (pt)
REVERT: C  315 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6853 (mp0)
REVERT: C  326 LYS cc_start: 0.8071 (tptp) cc_final: 0.7717 (tptp)
REVERT: C  382 SER cc_start: 0.7787 (t) cc_final: 0.7488 (p)
REVERT: C  383 ARG cc_start: 0.5861 (mmt180) cc_final: 0.5603 (mmm160)
REVERT: C  391 PHE cc_start: 0.7836 (t80) cc_final: 0.7612 (t80)
REVERT: C  430 ARG cc_start: 0.6146 (ttm170) cc_final: 0.5632 (ttm170)
REVERT: C  438 ARG cc_start: 0.7745 (mmt90) cc_final: 0.7483 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7958 (mmmt)
REVERT: D   64 MET cc_start: 0.7423 (mtp) cc_final: 0.7189 (mtp)
REVERT: D   78 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7786 (ttm-80)
REVERT: D   83 GLU cc_start: 0.7660 (tp30) cc_final: 0.7267 (tp30)
REVERT: D   88 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7262 (tppt)
REVERT: D  124 MET cc_start: 0.6546 (tmm) cc_final: 0.6098 (tmm)
REVERT: D  125 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7454 (t80)
REVERT: D  149 ASP cc_start: 0.7182 (t0) cc_final: 0.6827 (t0)
REVERT: D  152 VAL cc_start: 0.7016 (OUTLIER) cc_final: 0.6574 (p)
REVERT: D  163 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7329 (mm-40)
REVERT: D  167 ASP cc_start: 0.7527 (m-30) cc_final: 0.7178 (m-30)
REVERT: D  219 MET cc_start: 0.6755 (tmm) cc_final: 0.6412 (tmm)
REVERT: D  223 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7728 (tmtt)
REVERT: D  236 LYS cc_start: 0.8079 (tmmt) cc_final: 0.7638 (pttp)
REVERT: D  247 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7424 (ttm-80)
REVERT: D  262 LYS cc_start: 0.7259 (mmtm) cc_final: 0.7012 (mmtm)
REVERT: D  267 GLU cc_start: 0.7723 (tp30) cc_final: 0.7187 (tp30)
REVERT: D  279 MET cc_start: 0.5920 (mtm) cc_final: 0.5623 (ptt)
REVERT: D  315 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6999 (mm-30)
REVERT: D  323 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6558 (tm-30)
REVERT: D  367 LYS cc_start: 0.8230 (tptt) cc_final: 0.7710 (tptt)
REVERT: D  416 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.6245 (mmm)
REVERT: D  424 GLU cc_start: 0.7271 (tp30) cc_final: 0.6784 (tp30)
REVERT: D  434 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7150 (tm-30)
REVERT: D  442 THR cc_start: 0.6853 (OUTLIER) cc_final: 0.6322 (t)
REVERT: D  457 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7892 (mmmt)
REVERT: K   27 TYR cc_start: 0.8415 (m-10) cc_final: 0.8196 (m-10)
REVERT: K   92 LEU cc_start: 0.7682 (mm) cc_final: 0.7450 (mp)
REVERT: K  104 ILE cc_start: 0.8679 (tt) cc_final: 0.8477 (tt)
REVERT: K  105 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7828 (mp)
REVERT: K  125 VAL cc_start: 0.7309 (t) cc_final: 0.7009 (p)
REVERT: K  154 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6756 (p0)
REVERT: L   38 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7334 (mtm-85)
REVERT: L  122 GLU cc_start: 0.6929 (pm20) cc_final: 0.6631 (pm20)
REVERT: L  129 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7617 (tp40)
REVERT: L  169 GLU cc_start: 0.7411 (pp20) cc_final: 0.7148 (pp20)
  outliers start: 71
  outliers final: 48
  residues processed: 361
  average time/residue: 0.1168
  time to fit residues: 55.7518
Evaluate side-chains
  392 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 333
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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   85 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  163 GLN
Chi-restraints excluded: chain C residue  204 ASP
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  352 PHE
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  455 ILE
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  477 MET
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  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  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  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  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   55 VAL
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  129 GLN
Chi-restraints excluded: chain L residue  136 ILE
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 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 19 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3953 r_free = 0.3953 target = 0.140698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.126220 restraints weight = 18630.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.129890 restraints weight = 9092.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.132239 restraints weight = 5228.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.133656 restraints weight = 3379.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.134670 restraints weight = 2450.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10067  Z= 0.174
  Angle     :  0.653  17.932  13507  Z= 0.349
  Chirality :  0.041   0.293   1515
  Planarity :  0.003   0.038   1726
  Dihedral  :  4.552  55.566   1323
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 30.67 %
    Favored  : 63.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1173
  helix:  1.27 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.01 (0.40), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  46 
 TYR   0.024   0.002   TYR C 125 
 PHE   0.036   0.002   PHE C 377 
 TRP   0.039   0.003   TRP L 146 
 HIS   0.003   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (10067)
  covalent geometry    : angle       0.65310 (13507)
  hydrogen bonds       : bond        0.04113 (  630)
  hydrogen bonds       : angle       4.44203 ( 1878)

*********************** 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
  413 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 343
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7627 (mm-30)
REVERT: C   83 GLU cc_start: 0.7650 (tp30) cc_final: 0.7091 (tp30)
REVERT: C   91 GLU cc_start: 0.7466 (pm20) cc_final: 0.7028 (pm20)
REVERT: C  124 MET cc_start: 0.6733 (tmm) cc_final: 0.6336 (tmm)
REVERT: C  125 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7623 (t80)
REVERT: C  150 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7569 (mm-40)
REVERT: C  159 ASP cc_start: 0.7439 (t70) cc_final: 0.6339 (t0)
REVERT: C  163 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6225 (mp10)
REVERT: C  173 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7681 (mtt90)
REVERT: C  179 ASP cc_start: 0.8065 (p0) cc_final: 0.7656 (p0)
REVERT: C  183 ILE cc_start: 0.8536 (pt) cc_final: 0.8331 (tt)
REVERT: C  218 GLN cc_start: 0.7695 (pp30) cc_final: 0.7383 (pp30)
REVERT: C  262 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7396 (mmtm)
REVERT: C  269 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6897 (pt)
REVERT: C  315 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6829 (mp0)
REVERT: C  326 LYS cc_start: 0.8065 (tptp) cc_final: 0.7714 (tptp)
REVERT: C  382 SER cc_start: 0.7897 (t) cc_final: 0.7589 (p)
REVERT: C  383 ARG cc_start: 0.5869 (mmt180) cc_final: 0.5444 (mmp-170)
REVERT: C  430 ARG cc_start: 0.6156 (ttm170) cc_final: 0.5568 (ttm170)
REVERT: C  438 ARG cc_start: 0.7702 (mmt90) cc_final: 0.7395 (mmt90)
REVERT: C  457 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7909 (mmmt)
REVERT: D   64 MET cc_start: 0.7443 (mtp) cc_final: 0.7219 (mtp)
REVERT: D   83 GLU cc_start: 0.7665 (tp30) cc_final: 0.7234 (tp30)
REVERT: D   88 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7268 (tppt)
REVERT: D   90 ARG cc_start: 0.8388 (ttt180) cc_final: 0.8178 (ttt180)
REVERT: D  124 MET cc_start: 0.6546 (tmm) cc_final: 0.6085 (tmm)
REVERT: D  125 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7405 (t80)
REVERT: D  149 ASP cc_start: 0.7100 (t0) cc_final: 0.6831 (t0)
REVERT: D  163 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7311 (mm-40)
REVERT: D  167 ASP cc_start: 0.7543 (m-30) cc_final: 0.7178 (m-30)
REVERT: D  219 MET cc_start: 0.6744 (tmm) cc_final: 0.6368 (tmm)
REVERT: D  223 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7699 (tmtt)
REVERT: D  236 LYS cc_start: 0.8142 (tmmt) cc_final: 0.7678 (pttp)
REVERT: D  262 LYS cc_start: 0.7285 (mmtm) cc_final: 0.7030 (mmtm)
REVERT: D  267 GLU cc_start: 0.7726 (tp30) cc_final: 0.7207 (tp30)
REVERT: D  279 MET cc_start: 0.5884 (mtm) cc_final: 0.5567 (ptt)
REVERT: D  315 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6971 (mm-30)
REVERT: D  323 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: D  367 LYS cc_start: 0.8220 (tptt) cc_final: 0.7671 (tptt)
REVERT: D  416 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6285 (mmm)
REVERT: D  424 GLU cc_start: 0.7276 (tp30) cc_final: 0.6821 (tp30)
REVERT: D  425 LYS cc_start: 0.7096 (mtpt) cc_final: 0.6882 (mtpt)
REVERT: D  434 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7150 (tm-30)
REVERT: D  442 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6288 (t)
REVERT: D  457 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7900 (mmmt)
REVERT: K   92 LEU cc_start: 0.7645 (mm) cc_final: 0.7401 (mp)
REVERT: K  169 GLU cc_start: 0.7510 (pp20) cc_final: 0.7242 (pp20)
REVERT: L   78 MET cc_start: 0.7332 (ttt) cc_final: 0.7035 (ttp)
REVERT: L   79 PHE cc_start: 0.7777 (m-10) cc_final: 0.7533 (m-10)
REVERT: L  122 GLU cc_start: 0.6899 (pm20) cc_final: 0.6605 (pm20)
REVERT: L  129 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7602 (tp40)
  outliers start: 70
  outliers final: 49
  residues processed: 370
  average time/residue: 0.1231
  time to fit residues: 60.5339
Evaluate side-chains
  390 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 332
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
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   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  163 GLN
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  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  424 GLU
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  125 TYR
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  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  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   55 VAL
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  129 GLN
Chi-restraints excluded: chain L residue  136 ILE
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 109 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 118 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0670
   chunk 38 optimal weight:    3.9990
   chunk 56 optimal weight:    0.1980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3954 r_free = 0.3954 target = 0.140690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.126051 restraints weight = 18580.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.129719 restraints weight = 9119.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.132082 restraints weight = 5265.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.133626 restraints weight = 3409.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.134642 restraints weight = 2432.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10067  Z= 0.170
  Angle     :  0.666  17.791  13507  Z= 0.354
  Chirality :  0.041   0.290   1515
  Planarity :  0.003   0.029   1726
  Dihedral  :  4.467  56.372   1321
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 31.12 %
    Favored  : 61.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.26), residues: 1173
  helix:  1.28 (0.18), residues: 877
  sheet:  None (None), residues: 0
  loop : -1.03 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  46 
 TYR   0.016   0.001   TYR D  29 
 PHE   0.037   0.002   PHE D 377 
 TRP   0.039   0.003   TRP L 146 
 HIS   0.003   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10067)
  covalent geometry    : angle       0.66644 (13507)
  hydrogen bonds       : bond        0.04081 (  630)
  hydrogen bonds       : angle       4.43012 ( 1878)

*********************** 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
  420 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 343
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7639 (mm-30)
REVERT: C   83 GLU cc_start: 0.7624 (tp30) cc_final: 0.7069 (tp30)
REVERT: C   90 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8069 (ttt90)
REVERT: C   91 GLU cc_start: 0.7424 (pm20) cc_final: 0.6986 (pm20)
REVERT: C  124 MET cc_start: 0.6729 (tmm) cc_final: 0.6424 (tmm)
REVERT: C  125 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7600 (t80)
REVERT: C  150 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7639 (mm-40)
REVERT: C  159 ASP cc_start: 0.7430 (t70) cc_final: 0.6414 (t0)
REVERT: C  163 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6382 (mp10)
REVERT: C  173 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7646 (mtt180)
REVERT: C  179 ASP cc_start: 0.8063 (p0) cc_final: 0.7634 (p0)
REVERT: C  183 ILE cc_start: 0.8573 (pt) cc_final: 0.8361 (tt)
REVERT: C  218 GLN cc_start: 0.7685 (pp30) cc_final: 0.7353 (pp30)
REVERT: C  262 LYS cc_start: 0.7678 (mmtm) cc_final: 0.7395 (mmtm)
REVERT: C  269 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7032 (pt)
REVERT: C  315 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6831 (mp0)
REVERT: C  326 LYS cc_start: 0.8058 (tptp) cc_final: 0.7636 (tptp)
REVERT: C  330 SER cc_start: 0.8451 (m) cc_final: 0.7953 (m)
REVERT: C  381 ASN cc_start: 0.6932 (t0) cc_final: 0.6441 (t0)
REVERT: C  382 SER cc_start: 0.7952 (t) cc_final: 0.7564 (p)
REVERT: C  430 ARG cc_start: 0.6213 (ttm170) cc_final: 0.5700 (ttm170)
REVERT: C  438 ARG cc_start: 0.7693 (mmt90) cc_final: 0.7378 (mmt90)
REVERT: C  457 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7956 (mmmt)
REVERT: C  473 MET cc_start: 0.2571 (mmm) cc_final: 0.2298 (mmm)
REVERT: D   64 MET cc_start: 0.7451 (mtp) cc_final: 0.7234 (mtp)
REVERT: D   83 GLU cc_start: 0.7667 (tp30) cc_final: 0.7183 (tp30)
REVERT: D   88 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7269 (tppt)
REVERT: D   90 ARG cc_start: 0.8358 (ttt180) cc_final: 0.8098 (ttt180)
REVERT: D  124 MET cc_start: 0.6515 (tmm) cc_final: 0.6038 (tmm)
REVERT: D  125 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7304 (t80)
REVERT: D  149 ASP cc_start: 0.7120 (t0) cc_final: 0.6849 (t0)
REVERT: D  162 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8279 (ttp80)
REVERT: D  163 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7275 (mm-40)
REVERT: D  167 ASP cc_start: 0.7547 (m-30) cc_final: 0.7177 (m-30)
REVERT: D  219 MET cc_start: 0.6722 (tmm) cc_final: 0.6321 (tmm)
REVERT: D  223 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7698 (tmtt)
REVERT: D  236 LYS cc_start: 0.8189 (tmmt) cc_final: 0.7679 (pttp)
REVERT: D  262 LYS cc_start: 0.7265 (mmtm) cc_final: 0.7010 (mmtm)
REVERT: D  267 GLU cc_start: 0.7716 (tp30) cc_final: 0.7192 (tp30)
REVERT: D  315 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6965 (mm-30)
REVERT: D  323 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6505 (tm-30)
REVERT: D  367 LYS cc_start: 0.8210 (tptt) cc_final: 0.7685 (tptt)
REVERT: D  416 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6288 (mmm)
REVERT: D  434 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7165 (tm-30)
REVERT: D  442 THR cc_start: 0.6812 (OUTLIER) cc_final: 0.6280 (t)
REVERT: D  457 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7879 (mmmt)
REVERT: K   92 LEU cc_start: 0.7611 (mm) cc_final: 0.7393 (mp)
REVERT: K  105 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7939 (mp)
REVERT: K  125 VAL cc_start: 0.7283 (t) cc_final: 0.7073 (p)
REVERT: K  129 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7509 (tp40)
REVERT: K  154 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6555 (p0)
REVERT: L   54 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7544 (mp)
REVERT: L  129 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7564 (tp40)
REVERT: L  169 GLU cc_start: 0.7409 (pp20) cc_final: 0.7126 (pp20)
  outliers start: 77
  outliers final: 53
  residues processed: 375
  average time/residue: 0.1257
  time to fit residues: 62.8318
Evaluate side-chains
  403 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 337
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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   90 ARG
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  163 GLN
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  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  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   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  125 TYR
Chi-restraints excluded: chain D residue  183 ILE
Chi-restraints excluded: chain D residue  193 LEU
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  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   54 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   91 VAL
Chi-restraints excluded: chain L residue  129 GLN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0370
   chunk 103 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 6 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
D 250 HIS
D 381 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.141558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.127149 restraints weight = 18632.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.130789 restraints weight = 9046.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.133131 restraints weight = 5187.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.134423 restraints weight = 3365.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.135423 restraints weight = 2459.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10067  Z= 0.189
  Angle     :  0.689  17.964  13507  Z= 0.366
  Chirality :  0.042   0.292   1515
  Planarity :  0.003   0.029   1726
  Dihedral  :  4.534  55.151   1321
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  7.01 %
    Allowed  : 30.85 %
    Favored  : 62.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.26), residues: 1173
  helix:  1.22 (0.18), residues: 884
  sheet:  None (None), residues: 0
  loop : -1.04 (0.41), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 153 
 TYR   0.016   0.002   TYR D  29 
 PHE   0.029   0.002   PHE C  21 
 TRP   0.021   0.002   TRP L 146 
 HIS   0.004   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (10067)
  covalent geometry    : angle       0.68944 (13507)
  hydrogen bonds       : bond        0.04164 (  630)
  hydrogen bonds       : angle       4.46087 ( 1878)

*********************** 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
  433 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 355
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: C   46 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7636 (mtp-110)
REVERT: C   78 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7670 (ttm-80)
REVERT: C   83 GLU cc_start: 0.7637 (tp30) cc_final: 0.7070 (tp30)
REVERT: C   91 GLU cc_start: 0.7437 (pm20) cc_final: 0.6998 (pm20)
REVERT: C  124 MET cc_start: 0.6769 (tmm) cc_final: 0.6390 (tmm)
REVERT: C  125 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7663 (t80)
REVERT: C  128 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7299 (mmm-85)
REVERT: C  159 ASP cc_start: 0.7456 (t70) cc_final: 0.7045 (t70)
REVERT: C  163 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7026 (mp10)
REVERT: C  173 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7869 (mtt180)
REVERT: C  218 GLN cc_start: 0.7740 (pp30) cc_final: 0.7451 (pp30)
REVERT: C  262 LYS cc_start: 0.7680 (mmtm) cc_final: 0.7408 (mmtm)
REVERT: C  315 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6824 (mp0)
REVERT: C  326 LYS cc_start: 0.8074 (tptp) cc_final: 0.7818 (tptp)
REVERT: C  330 SER cc_start: 0.8469 (m) cc_final: 0.8063 (p)
REVERT: C  381 ASN cc_start: 0.6976 (t0) cc_final: 0.6492 (t0)
REVERT: C  382 SER cc_start: 0.7952 (t) cc_final: 0.7637 (p)
REVERT: C  430 ARG cc_start: 0.6236 (ttm170) cc_final: 0.5500 (ttm170)
REVERT: C  438 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7469 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7964 (mmmt)
REVERT: D   64 MET cc_start: 0.7484 (mtp) cc_final: 0.7265 (mtp)
REVERT: D   83 GLU cc_start: 0.7653 (tp30) cc_final: 0.7151 (tp30)
REVERT: D   88 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7327 (tppt)
REVERT: D   90 ARG cc_start: 0.8339 (ttt180) cc_final: 0.7990 (ttt180)
REVERT: D  124 MET cc_start: 0.6530 (tmm) cc_final: 0.6060 (tmm)
REVERT: D  125 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7355 (t80)
REVERT: D  149 ASP cc_start: 0.7199 (t0) cc_final: 0.6844 (t0)
REVERT: D  150 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7638 (mm110)
REVERT: D  162 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8519 (ttp80)
REVERT: D  163 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7333 (mm-40)
REVERT: D  167 ASP cc_start: 0.7546 (m-30) cc_final: 0.7175 (m-30)
REVERT: D  219 MET cc_start: 0.6753 (tmm) cc_final: 0.6327 (tmm)
REVERT: D  223 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7702 (tmtt)
REVERT: D  236 LYS cc_start: 0.8237 (tmmt) cc_final: 0.7722 (pttp)
REVERT: D  240 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.7465 (tpp-160)
REVERT: D  262 LYS cc_start: 0.7257 (mmtm) cc_final: 0.7010 (mmtm)
REVERT: D  267 GLU cc_start: 0.7757 (tp30) cc_final: 0.7164 (tp30)
REVERT: D  315 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6974 (mm-30)
REVERT: D  323 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6446 (tm-30)
REVERT: D  367 LYS cc_start: 0.8252 (tptt) cc_final: 0.7711 (tptt)
REVERT: D  416 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6279 (mmm)
REVERT: D  434 GLN cc_start: 0.7473 (tm-30) cc_final: 0.6520 (tm-30)
REVERT: D  438 ARG cc_start: 0.7874 (mmt90) cc_final: 0.7353 (mmt90)
REVERT: D  442 THR cc_start: 0.6826 (OUTLIER) cc_final: 0.6292 (t)
REVERT: D  457 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7893 (mmmt)
REVERT: K   78 MET cc_start: 0.7774 (ttm) cc_final: 0.6421 (tpp)
REVERT: K   85 GLU cc_start: 0.7703 (tt0) cc_final: 0.6538 (tt0)
REVERT: K  125 VAL cc_start: 0.7342 (t) cc_final: 0.7087 (p)
REVERT: K  129 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7570 (tp40)
REVERT: K  154 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6586 (p0)
REVERT: L  129 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7604 (tp40)
REVERT: L  154 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6768 (p0)
  outliers start: 78
  outliers final: 53
  residues processed: 385
  average time/residue: 0.1297
  time to fit residues: 65.9912
Evaluate side-chains
  411 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 348
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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  163 GLN
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  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  345 LEU
Chi-restraints excluded: chain C residue  352 PHE
Chi-restraints excluded: chain C residue  355 PHE
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   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  125 TYR
Chi-restraints excluded: chain D residue  183 ILE
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  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  129 GLN
Chi-restraints excluded: chain L residue  134 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 64 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 99 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.139671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.125285 restraints weight = 18492.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.128898 restraints weight = 9060.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.131198 restraints weight = 5231.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.132702 restraints weight = 3405.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.133521 restraints weight = 2434.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10067  Z= 0.197
  Angle     :  0.716  17.940  13507  Z= 0.377
  Chirality :  0.043   0.292   1515
  Planarity :  0.003   0.043   1726
  Dihedral  :  4.591  57.201   1321
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 32.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.26), residues: 1173
  helix:  1.17 (0.18), residues: 886
  sheet:  None (None), residues: 0
  loop : -1.05 (0.41), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 439 
 TYR   0.016   0.002   TYR D  29 
 PHE   0.031   0.002   PHE C  21 
 TRP   0.012   0.002   TRP L 146 
 HIS   0.004   0.001   HIS D 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (10067)
  covalent geometry    : angle       0.71630 (13507)
  hydrogen bonds       : bond        0.04207 (  630)
  hydrogen bonds       : angle       4.49247 ( 1878)

*********************** 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
  414 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 349
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7480 (mm-30)
REVERT: C   46 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7651 (mtp-110)
REVERT: C   78 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7685 (ttm-80)
REVERT: C   83 GLU cc_start: 0.7629 (tp30) cc_final: 0.7094 (tp30)
REVERT: C   91 GLU cc_start: 0.7449 (pm20) cc_final: 0.7009 (pm20)
REVERT: C  124 MET cc_start: 0.6709 (tmm) cc_final: 0.6416 (tmm)
REVERT: C  125 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7569 (t80)
REVERT: C  159 ASP cc_start: 0.7555 (t70) cc_final: 0.6622 (t70)
REVERT: C  163 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6503 (mp10)
REVERT: C  173 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7824 (mtt90)
REVERT: C  218 GLN cc_start: 0.7720 (pp30) cc_final: 0.7453 (pp30)
REVERT: C  223 LYS cc_start: 0.7813 (tptp) cc_final: 0.7450 (ttpp)
REVERT: C  224 PHE cc_start: 0.6987 (m-10) cc_final: 0.6013 (m-80)
REVERT: C  262 LYS cc_start: 0.7696 (mmtm) cc_final: 0.7404 (mmtm)
REVERT: C  315 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6820 (mp0)
REVERT: C  326 LYS cc_start: 0.8070 (tptp) cc_final: 0.7809 (tptp)
REVERT: C  330 SER cc_start: 0.8510 (m) cc_final: 0.8053 (p)
REVERT: C  381 ASN cc_start: 0.7016 (t0) cc_final: 0.6590 (t0)
REVERT: C  382 SER cc_start: 0.7990 (t) cc_final: 0.7580 (p)
REVERT: C  430 ARG cc_start: 0.6243 (ttm170) cc_final: 0.5144 (ttm-80)
REVERT: C  438 ARG cc_start: 0.7681 (mmt90) cc_final: 0.7431 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7967 (mmmt)
REVERT: D   62 TYR cc_start: 0.6819 (t80) cc_final: 0.6519 (t80)
REVERT: D   83 GLU cc_start: 0.7628 (tp30) cc_final: 0.7149 (tp30)
REVERT: D   88 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7309 (tppt)
REVERT: D   90 ARG cc_start: 0.8336 (ttt180) cc_final: 0.7998 (ttt180)
REVERT: D  124 MET cc_start: 0.6543 (tmm) cc_final: 0.6184 (tmm)
REVERT: D  125 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7652 (t80)
REVERT: D  149 ASP cc_start: 0.7190 (t0) cc_final: 0.6793 (t0)
REVERT: D  162 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8483 (ttp80)
REVERT: D  163 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7331 (mm-40)
REVERT: D  167 ASP cc_start: 0.7528 (m-30) cc_final: 0.7162 (m-30)
REVERT: D  223 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7706 (tmtt)
REVERT: D  236 LYS cc_start: 0.8254 (tmmt) cc_final: 0.7902 (ttpp)
REVERT: D  262 LYS cc_start: 0.7267 (mmtm) cc_final: 0.7019 (mmtm)
REVERT: D  267 GLU cc_start: 0.7755 (tp30) cc_final: 0.7176 (tp30)
REVERT: D  315 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6958 (mm-30)
REVERT: D  323 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6440 (tm-30)
REVERT: D  367 LYS cc_start: 0.8255 (tptt) cc_final: 0.7695 (tptt)
REVERT: D  416 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.6306 (mmm)
REVERT: D  434 GLN cc_start: 0.7477 (tm-30) cc_final: 0.6598 (tm-30)
REVERT: D  438 ARG cc_start: 0.7861 (mmt90) cc_final: 0.7340 (mmt90)
REVERT: D  442 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6309 (t)
REVERT: D  457 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7883 (mmmt)
REVERT: K   78 MET cc_start: 0.7696 (ttm) cc_final: 0.6287 (tpp)
REVERT: K   85 GLU cc_start: 0.7772 (tt0) cc_final: 0.6462 (tt0)
REVERT: K  129 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7565 (tp40)
REVERT: K  154 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6629 (p0)
REVERT: L   54 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7548 (mt)
REVERT: L  129 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7662 (tp40)
REVERT: L  154 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6783 (p0)
  outliers start: 65
  outliers final: 51
  residues processed: 368
  average time/residue: 0.1251
  time to fit residues: 60.8081
Evaluate side-chains
  409 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 347
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  163 GLN
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  273 MET
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  306 VAL
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  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   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  125 TYR
Chi-restraints excluded: chain D residue  183 ILE
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  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  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   54 LEU
Chi-restraints excluded: chain L residue   61 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  129 GLN
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 12 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 80 optimal weight:    0.3980
   chunk 104 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 286 HIS
** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 286 HIS
D 381 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.138485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.124229 restraints weight = 18520.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.127839 restraints weight = 9127.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.130112 restraints weight = 5273.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.131650 restraints weight = 3427.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.132600 restraints weight = 2430.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10067  Z= 0.239
  Angle     :  0.762  18.159  13507  Z= 0.402
  Chirality :  0.045   0.293   1515
  Planarity :  0.003   0.034   1726
  Dihedral  :  4.740  55.422   1321
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 32.10 %
    Favored  : 62.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.26), residues: 1173
  helix:  1.07 (0.18), residues: 880
  sheet:  None (None), residues: 0
  loop : -0.99 (0.41), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 439 
 TYR   0.017   0.002   TYR C  29 
 PHE   0.030   0.002   PHE C  21 
 TRP   0.010   0.002   TRP L 146 
 HIS   0.005   0.001   HIS D 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 (10067)
  covalent geometry    : angle       0.76221 (13507)
  hydrogen bonds       : bond        0.04471 (  630)
  hydrogen bonds       : angle       4.59940 ( 1878)

********************** 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
  418 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 353
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7593 (mm-30)
REVERT: C   46 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7691 (mtm-85)
REVERT: C   78 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7695 (ttm-80)
REVERT: C   83 GLU cc_start: 0.7673 (tp30) cc_final: 0.7099 (tp30)
REVERT: C   88 LYS cc_start: 0.8055 (tppt) cc_final: 0.7277 (tppt)
REVERT: C   91 GLU cc_start: 0.7451 (pm20) cc_final: 0.7122 (pm20)
REVERT: C  124 MET cc_start: 0.6745 (tmm) cc_final: 0.6427 (tmm)
REVERT: C  125 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7557 (t80)
REVERT: C  159 ASP cc_start: 0.7590 (t70) cc_final: 0.6712 (t70)
REVERT: C  163 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6561 (mp10)
REVERT: C  218 GLN cc_start: 0.7743 (pp30) cc_final: 0.7468 (pp30)
REVERT: C  219 MET cc_start: 0.6995 (mmm) cc_final: 0.6604 (mmm)
REVERT: C  262 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7424 (mmtm)
REVERT: C  315 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6857 (mp0)
REVERT: C  326 LYS cc_start: 0.8113 (tptp) cc_final: 0.7867 (tptp)
REVERT: C  330 SER cc_start: 0.8452 (m) cc_final: 0.7991 (p)
REVERT: C  381 ASN cc_start: 0.7087 (t0) cc_final: 0.6565 (t0)
REVERT: C  382 SER cc_start: 0.8053 (t) cc_final: 0.7632 (p)
REVERT: C  430 ARG cc_start: 0.6308 (ttm170) cc_final: 0.5380 (ttm-80)
REVERT: C  438 ARG cc_start: 0.7660 (mmt90) cc_final: 0.7409 (mmm-85)
REVERT: C  457 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7957 (mmmt)
REVERT: D   47 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8171 (mmmt)
REVERT: D   52 LEU cc_start: 0.8655 (mt) cc_final: 0.8442 (mt)
REVERT: D   83 GLU cc_start: 0.7688 (tp30) cc_final: 0.7086 (tp30)
REVERT: D   88 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7449 (tppt)
REVERT: D   90 ARG cc_start: 0.8315 (ttt180) cc_final: 0.8050 (ttt180)
REVERT: D  124 MET cc_start: 0.6579 (tmm) cc_final: 0.6061 (tmm)
REVERT: D  125 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7495 (t80)
REVERT: D  149 ASP cc_start: 0.7226 (t0) cc_final: 0.6808 (t0)
REVERT: D  162 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8462 (ttp80)
REVERT: D  163 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7330 (mm-40)
REVERT: D  167 ASP cc_start: 0.7522 (m-30) cc_final: 0.7167 (m-30)
REVERT: D  168 MET cc_start: 0.7454 (mtm) cc_final: 0.7212 (ttm)
REVERT: D  223 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7769 (tmtt)
REVERT: D  236 LYS cc_start: 0.8371 (tmmt) cc_final: 0.7765 (ttpp)
REVERT: D  240 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7477 (tpp-160)
REVERT: D  262 LYS cc_start: 0.7265 (mmtm) cc_final: 0.7004 (mmtm)
REVERT: D  267 GLU cc_start: 0.7793 (tp30) cc_final: 0.7435 (tp30)
REVERT: D  315 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6996 (mm-30)
REVERT: D  323 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6471 (tm-30)
REVERT: D  367 LYS cc_start: 0.8264 (tptt) cc_final: 0.7688 (tptt)
REVERT: D  416 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6327 (mmm)
REVERT: D  434 GLN cc_start: 0.7487 (tm-30) cc_final: 0.6554 (tm-30)
REVERT: D  438 ARG cc_start: 0.7849 (mmt90) cc_final: 0.7329 (mmt90)
REVERT: D  442 THR cc_start: 0.6888 (OUTLIER) cc_final: 0.6365 (t)
REVERT: D  457 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7888 (mmmt)
REVERT: K   78 MET cc_start: 0.7803 (ttm) cc_final: 0.6267 (tpp)
REVERT: K   79 PHE cc_start: 0.8084 (m-10) cc_final: 0.7811 (m-80)
REVERT: K   85 GLU cc_start: 0.7882 (tt0) cc_final: 0.6469 (tt0)
REVERT: K  125 VAL cc_start: 0.7725 (t) cc_final: 0.7508 (p)
REVERT: K  129 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7555 (tp40)
REVERT: K  154 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6612 (p0)
REVERT: L  154 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6778 (p0)
  outliers start: 65
  outliers final: 48
  residues processed: 372
  average time/residue: 0.1303
  time to fit residues: 63.8344
Evaluate side-chains
  410 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 353
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   29 TYR
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  163 GLN
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  236 LYS
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  287 MET
Chi-restraints excluded: chain C residue  306 VAL
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  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  125 TYR
Chi-restraints excluded: chain D residue  183 ILE
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  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  136 ILE
Chi-restraints excluded: chain K residue  154 ASP
Chi-restraints excluded: chain K residue  155 VAL
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  129 GLN
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 6 optimal weight:    0.0970
   chunk 68 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   chunk 80 optimal weight:    0.2980
   chunk 55 optimal weight:    0.9990
   chunk 72 optimal weight:    0.3980
   chunk 50 optimal weight:    0.2980
   chunk 75 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3378

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.141199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.126837 restraints weight = 18626.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.130525 restraints weight = 9098.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.132810 restraints weight = 5226.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.134383 restraints weight = 3391.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.135328 restraints weight = 2402.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.3484

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= 0.159
  Angle     :  0.732  17.602  13507  Z= 0.380
  Chirality :  0.042   0.284   1515
  Planarity :  0.003   0.054   1726
  Dihedral  :  4.604  55.346   1321
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 33.09 %
    Favored  : 61.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1173
  helix:  1.23 (0.18), residues: 879
  sheet:  None (None), residues: 0
  loop : -1.06 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  90 
 TYR   0.016   0.001   TYR K 174 
 PHE   0.039   0.002   PHE C 224 
 TRP   0.013   0.002   TRP C  34 
 HIS   0.002   0.001   HIS D 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10067)
  covalent geometry    : angle       0.73223 (13507)
  hydrogen bonds       : bond        0.03976 (  630)
  hydrogen bonds       : angle       4.50841 ( 1878)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2262.12 seconds
wall clock time: 39 minutes 47.51 seconds (2387.51 seconds total)