Starting phenix.real_space_refine
on Tue Apr 29 19:57:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuv_50779/04_2025/9fuv_50779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuv_50779/04_2025/9fuv_50779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuv_50779/04_2025/9fuv_50779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuv_50779/04_2025/9fuv_50779.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuv_50779/04_2025/9fuv_50779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuv_50779/04_2025/9fuv_50779.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 7.32, per 1000 atoms: 0.83
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (116.96, 101.32, 136.68, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.84
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      68.4% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 3.888A  pdb=" N   ILE A  35 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   MET A  44 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 3.549A  pdb=" N   ASP A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 111
      removed outlier: 3.943A  pdb=" N   TRP A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
      removed outlier: 3.554A  pdb=" N   GLY A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 129
      removed outlier: 3.974A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 164
      removed outlier: 3.852A  pdb=" N   GLU A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLY A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 213
      Proline residue:  A 176  - end of helix
      removed outlier: 3.637A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 3.553A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 269
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 281 through 323
      removed outlier: 4.086A  pdb=" N   THR A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.592A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.535A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 3.852A  pdb=" N   ALA A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 4.086A  pdb=" N   ILE A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.764A  pdb=" N   THR A 472 " --> pdb=" O   GLY A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 538 through 545
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 16 through 21
    Processing helix  chain 'B' and resid 23 through 55
      removed outlier: 4.419A  pdb=" N   ASP B  41 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU B  48 " --> pdb=" O   MET B  44 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 61 through 110
      removed outlier: 4.188A  pdb=" N   TRP B  66 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.970A  pdb=" N   THR B  99 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 129
    Processing helix  chain 'B' and resid 129 through 147
    Processing helix  chain 'B' and resid 147 through 164
    Processing helix  chain 'B' and resid 166 through 173
    Processing helix  chain 'B' and resid 173 through 213
      removed outlier: 4.111A  pdb=" N   ILE B 177 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 220
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 3.898A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 281 through 323
      removed outlier: 3.785A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 4.239A  pdb=" N   ASN B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA B 313 " --> pdb=" O   GLN B 309 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ALA B 314 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   CYS B 315 " --> pdb=" O   GLY B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 391
      removed outlier: 3.837A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 457
      removed outlier: 3.669A  pdb=" N   ILE B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU B 451 " --> pdb=" O   ARG B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 4.363A  pdb=" N   ILE B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 472
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 528
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.528A  pdb=" N   GLU A 343 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 3.510A  pdb=" N   ILE A 503 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 422 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 342 through 345
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.123A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU B 547 " --> pdb=" O   THR B 371 " (cutoff:3.500A)

    557 hydrogen bonds defined for protein.
    1650 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2867
        1.34 -     1.45: 1039
        1.45 -     1.57: 4940
        1.57 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   VAL A  65 "
       pdb=" CA  VAL A  65 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.23e+00
  bond pdb=" N   VAL B  63 "
       pdb=" CA  VAL B  63 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.29e-02 6.01e+03 7.39e+00
  bond pdb=" N   VAL B 356 "
       pdb=" CA  VAL B 356 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.23e-02 6.61e+03 7.30e+00
  bond pdb=" N   VAL A  63 "
       pdb=" CA  VAL A  63 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.26e-02 6.30e+03 7.16e+00
  bond pdb=" N   THR B 472 "
       pdb=" CA  THR B 472 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.22e-02 6.72e+03 7.11e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 11296
        1.23 -     2.47: 629
        2.47 -     3.70: 120
        3.70 -     4.93: 34
        4.93 -     6.16: 13
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   ALA B 358 "
        pdb=" CA  ALA B 358 "
        pdb=" C   ALA B 358 "
      ideal   model   delta    sigma   weight residual
     113.16  108.07    5.09 1.24e+00 6.50e-01 1.69e+01
  angle pdb=" C   THR B 472 "
        pdb=" CA  THR B 472 "
        pdb=" CB  THR B 472 "
      ideal   model   delta    sigma   weight residual
     109.89  103.73    6.16 1.60e+00 3.91e-01 1.48e+01
  angle pdb=" N   ASP B 341 "
        pdb=" CA  ASP B 341 "
        pdb=" C   ASP B 341 "
      ideal   model   delta    sigma   weight residual
     109.59  115.16   -5.57 1.47e+00 4.63e-01 1.44e+01
  angle pdb=" N   GLU B 327 "
        pdb=" CA  GLU B 327 "
        pdb=" CB  GLU B 327 "
      ideal   model   delta    sigma   weight residual
     109.19  114.76   -5.57 1.54e+00 4.22e-01 1.31e+01
  angle pdb=" N   LEU B 125 "
        pdb=" CA  LEU B 125 "
        pdb=" C   LEU B 125 "
      ideal   model   delta    sigma   weight residual
     111.36  107.53    3.83 1.09e+00 8.42e-01 1.24e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 4614
       16.94 -    33.87: 610
       33.87 -    50.81: 184
       50.81 -    67.74: 37
       67.74 -    84.68: 9
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  TRP A  17 "
           pdb=" C   TRP A  17 "
           pdb=" N   PRO A  18 "
           pdb=" CA  PRO A  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.51   23.49     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  PHE A 272 "
           pdb=" C   PHE A 272 "
           pdb=" N   PRO A 273 "
           pdb=" CA  PRO A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  PHE A  13 "
           pdb=" C   PHE A  13 "
           pdb=" N   ARG A  14 "
           pdb=" CA  ARG A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.12   19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1034
       0.036 -    0.073: 286
       0.073 -    0.109: 90
       0.109 -    0.146: 21
       0.146 -    0.182: 9
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  LEU B 125 "
            pdb=" N   LEU B 125 "
            pdb=" C   LEU B 125 "
            pdb=" CB  LEU B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.27e-01
  chirality pdb=" CA  VAL A  63 "
            pdb=" N   VAL A  63 "
            pdb=" C   VAL A  63 "
            pdb=" CB  VAL A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.07e-01
  chirality pdb=" CB  VAL A  63 "
            pdb=" CA  VAL A  63 "
            pdb=" CG1 VAL A  63 "
            pdb=" CG2 VAL A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.02e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 296 "    0.051 5.00e-02 4.00e+02   7.63e-02 9.32e+00
        pdb=" N   PRO A 297 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 297 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 297 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  49 "    0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO B  50 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B  50 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B  50 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 133 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   GLU B 133 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLU B 133 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLN B 134 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 866
        2.73 -     3.27: 10297
        3.27 -     3.82: 15382
        3.82 -     4.36: 17502
        4.36 -     4.90: 28205
  Nonbonded interactions: 72252
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 467 "
            pdb=" N   ASN A 468 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" O   GLY A 282 "
            pdb=" OG1 THR A 285 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLN A 202 "
            pdb=" OG1 THR A 205 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OD1 ASP A 231 "
            pdb=" NH2 ARG B 102 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" O   ARG A 377 "
            pdb=" NE  ARG A 377 "
     model   vdw
     2.250 3.120
  ... (remaining 72247 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     27.370
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
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      :  0.004   0.037   8950  Z= 0.214
  Angle     :  0.690   6.163  12092  Z= 0.407
  Chirality :  0.041   0.182   1440
  Planarity :  0.005   0.076   1532
  Dihedral  : 17.155  84.677   3326
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.03 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 31.30 %
    Favored  : 68.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.25), residues: 1134
  helix:  0.93 (0.20), residues: 702
  sheet: -1.16 (0.75), residues: 56
  loop : -1.65 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  91 
 HIS   0.006   0.001   HIS B 214 
 PHE   0.014   0.002   PHE A  56 
 TYR   0.013   0.001   TYR B 439 
 ARG   0.009   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15279 (  557)
  hydrogen bonds       : angle       6.71115 ( 1650)
  covalent geometry    : bond        0.00369 ( 8950)
  covalent geometry    : angle       0.68965 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 163
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8210 (tpp) cc_final: 0.7934 (ttt)
REVERT: A  149 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7784 (mm-30)
REVERT: A  295 MET cc_start: 0.8203 (ttm) cc_final: 0.7915 (ttm)
REVERT: A  312 MET cc_start: 0.8618 (mmm) cc_final: 0.8100 (mmm)
REVERT: A  495 LEU cc_start: 0.9092 (mm) cc_final: 0.8859 (mm)
REVERT: B   98 MET cc_start: 0.8232 (ppp) cc_final: 0.7793 (tmm)
REVERT: B  456 MET cc_start: 0.9047 (ttp) cc_final: 0.8841 (ptm)
REVERT: B  481 LEU cc_start: 0.8859 (mt) cc_final: 0.8525 (pt)
REVERT: B  495 LEU cc_start: 0.9042 (tt) cc_final: 0.8806 (tt)
  outliers start: 6
  outliers final: 3
  residues processed: 167
  average time/residue: 0.2233
  time to fit residues: 52.9913
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 1.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 84 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
B 363 ASN
B 430 ASN
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 562 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.099838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.077328 restraints weight = 29136.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.079705 restraints weight = 15966.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.081341 restraints weight = 10693.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8950  Z= 0.145
  Angle     :  0.650  10.171  12092  Z= 0.337
  Chirality :  0.042   0.176   1440
  Planarity :  0.004   0.046   1532
  Dihedral  :  5.156  56.192   1243
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.23 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 29.13 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1134
  helix:  1.06 (0.19), residues: 726
  sheet: -0.87 (0.85), residues: 44
  loop : -1.60 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 165 
 HIS   0.008   0.002   HIS A 214 
 PHE   0.017   0.002   PHE A  23 
 TYR   0.020   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  557)
  hydrogen bonds       : angle       4.82313 ( 1650)
  covalent geometry    : bond        0.00304 ( 8950)
  covalent geometry    : angle       0.65040 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 173
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8846 (tpp) cc_final: 0.8482 (tpp)
REVERT: A  108 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8300 (mtt)
REVERT: A  111 MET cc_start: 0.8448 (tpp) cc_final: 0.8119 (ttt)
REVERT: A  295 MET cc_start: 0.8161 (ttm) cc_final: 0.7879 (ttm)
REVERT: A  495 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: B   98 MET cc_start: 0.8487 (ppp) cc_final: 0.7924 (tmm)
REVERT: B  133 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7518 (tm-30)
REVERT: B  325 GLU cc_start: 0.7843 (pm20) cc_final: 0.7611 (pm20)
REVERT: B  428 LEU cc_start: 0.9118 (tp) cc_final: 0.8779 (tp)
REVERT: B  481 LEU cc_start: 0.8843 (mt) cc_final: 0.8558 (pt)
  outliers start: 37
  outliers final: 18
  residues processed: 196
  average time/residue: 0.2298
  time to fit residues: 64.2519
Evaluate side-chains
  168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  524 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 82 optimal weight:    0.1980
   overall best weight:    0.6962

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 579 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.101049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.078227 restraints weight = 29522.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.080590 restraints weight = 16384.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.082217 restraints weight = 11047.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8950  Z= 0.133
  Angle     :  0.618  10.138  12092  Z= 0.319
  Chirality :  0.042   0.184   1440
  Planarity :  0.004   0.036   1532
  Dihedral  :  4.831  48.414   1241
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.41 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 28.82 %
    Favored  : 66.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.25), residues: 1134
  helix:  1.13 (0.19), residues: 728
  sheet: -0.79 (0.83), residues: 44
  loop : -1.61 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  66 
 HIS   0.012   0.001   HIS B 214 
 PHE   0.015   0.002   PHE A  23 
 TYR   0.017   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  557)
  hydrogen bonds       : angle       4.50400 ( 1650)
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.61846 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 161
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.6185 (mmp) cc_final: 0.5879 (mmt)
REVERT: A   98 MET cc_start: 0.8904 (tpp) cc_final: 0.8344 (tpp)
REVERT: A  111 MET cc_start: 0.8317 (tpp) cc_final: 0.8103 (ttt)
REVERT: A  149 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7540 (mm-30)
REVERT: A  209 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8024 (mp10)
REVERT: A  295 MET cc_start: 0.8162 (ttm) cc_final: 0.7857 (ttm)
REVERT: A  495 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8713 (mm)
REVERT: B   98 MET cc_start: 0.8543 (ppp) cc_final: 0.8213 (tmm)
REVERT: B  107 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.8022 (t-90)
REVERT: B  133 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8083 (tm-30)
REVERT: B  149 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7514 (mm-30)
REVERT: B  481 LEU cc_start: 0.8830 (mt) cc_final: 0.8514 (pt)
  outliers start: 50
  outliers final: 30
  residues processed: 198
  average time/residue: 0.1865
  time to fit residues: 53.1670
Evaluate side-chains
  180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  491 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 92 optimal weight:   20.0000
   chunk 99 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.099311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.076448 restraints weight = 29590.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.078729 restraints weight = 16753.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.080313 restraints weight = 11433.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8950  Z= 0.162
  Angle     :  0.655  10.391  12092  Z= 0.335
  Chirality :  0.042   0.176   1440
  Planarity :  0.004   0.036   1532
  Dihedral  :  4.879  54.715   1241
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.85 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 29.75 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1134
  helix:  1.17 (0.19), residues: 730
  sheet: -0.90 (0.82), residues: 44
  loop : -1.60 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  17 
 HIS   0.009   0.002   HIS A 214 
 PHE   0.018   0.002   PHE A  23 
 TYR   0.019   0.001   TYR A 439 
 ARG   0.004   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04370 (  557)
  hydrogen bonds       : angle       4.44675 ( 1650)
  covalent geometry    : bond        0.00362 ( 8950)
  covalent geometry    : angle       0.65467 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 154
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8906 (tpp) cc_final: 0.8233 (tpp)
REVERT: A  149 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7627 (mm-30)
REVERT: A  224 GLU cc_start: 0.8746 (pm20) cc_final: 0.8452 (pp20)
REVERT: A  295 MET cc_start: 0.8101 (ttm) cc_final: 0.7785 (ttm)
REVERT: A  487 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8604 (tp40)
REVERT: A  495 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: A  517 ARG cc_start: 0.8981 (ttt180) cc_final: 0.8760 (ptp90)
REVERT: B  100 MET cc_start: 0.8913 (mmp) cc_final: 0.8638 (tpp)
REVERT: B  133 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8038 (tm-30)
REVERT: B  149 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7556 (mm-30)
REVERT: B  174 LEU cc_start: 0.9115 (mt) cc_final: 0.8889 (mp)
REVERT: B  428 LEU cc_start: 0.8990 (tp) cc_final: 0.8751 (tp)
REVERT: B  458 TYR cc_start: 0.8426 (t80) cc_final: 0.8109 (t80)
  outliers start: 49
  outliers final: 36
  residues processed: 188
  average time/residue: 0.1842
  time to fit residues: 50.1765
Evaluate side-chains
  186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 146
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  576 HIS
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 70 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.100041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.077278 restraints weight = 29306.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.079613 restraints weight = 16516.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.081157 restraints weight = 11234.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8950  Z= 0.138
  Angle     :  0.630  11.006  12092  Z= 0.320
  Chirality :  0.042   0.174   1440
  Planarity :  0.004   0.037   1532
  Dihedral  :  4.821  56.279   1241
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.59 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 29.24 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1134
  helix:  1.25 (0.19), residues: 730
  sheet: -0.86 (0.82), residues: 44
  loop : -1.64 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 165 
 HIS   0.010   0.001   HIS A 214 
 PHE   0.014   0.002   PHE A  23 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04186 (  557)
  hydrogen bonds       : angle       4.34034 ( 1650)
  covalent geometry    : bond        0.00304 ( 8950)
  covalent geometry    : angle       0.63034 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 155
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8883 (tpp) cc_final: 0.8207 (tpp)
REVERT: A  107 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.7428 (t-90)
REVERT: A  149 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7560 (mm-30)
REVERT: A  295 MET cc_start: 0.8049 (ttm) cc_final: 0.7731 (ttm)
REVERT: A  460 MET cc_start: 0.7912 (tpt) cc_final: 0.7602 (tmm)
REVERT: A  487 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8723 (tp40)
REVERT: A  495 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8696 (mm)
REVERT: A  517 ARG cc_start: 0.9006 (ttt180) cc_final: 0.8763 (ptp90)
REVERT: A  562 HIS cc_start: 0.8097 (p-80) cc_final: 0.7889 (p90)
REVERT: B   17 TRP cc_start: 0.6686 (OUTLIER) cc_final: 0.6484 (t60)
REVERT: B   98 MET cc_start: 0.8478 (tmm) cc_final: 0.8023 (tmm)
REVERT: B  100 MET cc_start: 0.8905 (mmp) cc_final: 0.8559 (tpp)
REVERT: B  107 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.8012 (t-90)
REVERT: B  133 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8047 (tm-30)
REVERT: B  149 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7587 (mm-30)
REVERT: B  160 MET cc_start: 0.8284 (tpp) cc_final: 0.7966 (tpp)
REVERT: B  174 LEU cc_start: 0.9114 (mt) cc_final: 0.8900 (mp)
REVERT: B  458 TYR cc_start: 0.8400 (t80) cc_final: 0.8128 (t80)
REVERT: B  481 LEU cc_start: 0.8417 (mm) cc_final: 0.8069 (mt)
REVERT: B  486 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (mtt90)
  outliers start: 51
  outliers final: 37
  residues processed: 192
  average time/residue: 0.1786
  time to fit residues: 49.6120
Evaluate side-chains
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 140
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 106 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 485 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 = 0.3631 r_free = 0.3631 target = 0.096472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.073660 restraints weight = 29428.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.075855 restraints weight = 16736.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.077413 restraints weight = 11480.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8950  Z= 0.192
  Angle     :  0.691  13.590  12092  Z= 0.351
  Chirality :  0.043   0.144   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  4.985  59.296   1241
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.29 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 29.24 %
    Favored  : 64.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.25), residues: 1134
  helix:  1.19 (0.19), residues: 730
  sheet: -1.59 (0.64), residues: 64
  loop : -1.60 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  17 
 HIS   0.009   0.002   HIS A 214 
 PHE   0.023   0.002   PHE A  23 
 TYR   0.026   0.002   TYR A 439 
 ARG   0.004   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04475 (  557)
  hydrogen bonds       : angle       4.53185 ( 1650)
  covalent geometry    : bond        0.00428 ( 8950)
  covalent geometry    : angle       0.69115 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 140
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8883 (tpp) cc_final: 0.8089 (tpp)
REVERT: A  107 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7495 (t-90)
REVERT: A  295 MET cc_start: 0.8121 (ttm) cc_final: 0.7760 (ttm)
REVERT: A  487 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8597 (tp40)
REVERT: A  495 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8746 (mm)
REVERT: A  517 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8770 (ptp90)
REVERT: B   98 MET cc_start: 0.8512 (tmm) cc_final: 0.8162 (tmm)
REVERT: B  100 MET cc_start: 0.8953 (mmp) cc_final: 0.8659 (tpp)
REVERT: B  107 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8111 (t-90)
REVERT: B  133 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7727 (tm-30)
REVERT: B  149 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7636 (mm-30)
REVERT: B  160 MET cc_start: 0.8467 (tpp) cc_final: 0.8127 (tpp)
REVERT: B  276 MET cc_start: 0.7396 (mmp) cc_final: 0.7195 (mmt)
REVERT: B  374 LEU cc_start: 0.9048 (mm) cc_final: 0.8687 (tp)
REVERT: B  481 LEU cc_start: 0.8585 (mm) cc_final: 0.8219 (mt)
REVERT: B  486 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8716 (mtt90)
  outliers start: 58
  outliers final: 47
  residues processed: 185
  average time/residue: 0.1756
  time to fit residues: 47.0667
Evaluate side-chains
  190 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 136
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  464 ASN
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  576 HIS
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.3980
   chunk 100 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.099062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.076431 restraints weight = 29642.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.078789 restraints weight = 16472.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.080461 restraints weight = 11098.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8950  Z= 0.130
  Angle     :  0.643  13.920  12092  Z= 0.321
  Chirality :  0.041   0.205   1440
  Planarity :  0.004   0.039   1532
  Dihedral  :  4.771  49.559   1241
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.41 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 30.68 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1134
  helix:  1.27 (0.19), residues: 730
  sheet: -1.38 (0.66), residues: 64
  loop : -1.62 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 165 
 HIS   0.015   0.001   HIS A 214 
 PHE   0.012   0.001   PHE A  23 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 (  557)
  hydrogen bonds       : angle       4.30806 ( 1650)
  covalent geometry    : bond        0.00286 ( 8950)
  covalent geometry    : angle       0.64295 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 150
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.6247 (mmt) cc_final: 0.5727 (mmt)
REVERT: A   98 MET cc_start: 0.8895 (tpp) cc_final: 0.8180 (tpp)
REVERT: A  107 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7399 (t-90)
REVERT: A  295 MET cc_start: 0.8025 (ttm) cc_final: 0.7683 (ttm)
REVERT: A  487 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8580 (tp40)
REVERT: A  495 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8698 (mm)
REVERT: A  517 ARG cc_start: 0.9028 (ttt180) cc_final: 0.8779 (ptp90)
REVERT: B  100 MET cc_start: 0.8898 (mmp) cc_final: 0.8659 (tpp)
REVERT: B  107 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8015 (t-90)
REVERT: B  133 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7771 (tm-30)
REVERT: B  149 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7640 (mm-30)
REVERT: B  160 MET cc_start: 0.8285 (tpp) cc_final: 0.8082 (tpp)
REVERT: B  374 LEU cc_start: 0.9070 (mm) cc_final: 0.8688 (tp)
REVERT: B  481 LEU cc_start: 0.8560 (mm) cc_final: 0.8156 (mt)
REVERT: B  486 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8697 (mtt90)
  outliers start: 53
  outliers final: 41
  residues processed: 186
  average time/residue: 0.1771
  time to fit residues: 46.9841
Evaluate side-chains
  189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 141
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 96 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.097607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.074621 restraints weight = 30172.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.076881 restraints weight = 17090.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.078474 restraints weight = 11705.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8950  Z= 0.169
  Angle     :  0.684  11.621  12092  Z= 0.345
  Chirality :  0.042   0.190   1440
  Planarity :  0.004   0.040   1532
  Dihedral  :  4.809  48.323   1241
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.85 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 30.68 %
    Favored  : 63.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1134
  helix:  1.24 (0.19), residues: 730
  sheet: -1.46 (0.63), residues: 64
  loop : -1.64 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  91 
 HIS   0.015   0.002   HIS A 214 
 PHE   0.020   0.002   PHE A  23 
 TYR   0.022   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04334 (  557)
  hydrogen bonds       : angle       4.41784 ( 1650)
  covalent geometry    : bond        0.00378 ( 8950)
  covalent geometry    : angle       0.68366 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 141
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.6364 (mmt) cc_final: 0.5820 (mmt)
REVERT: A   98 MET cc_start: 0.8869 (tpp) cc_final: 0.8088 (tpp)
REVERT: A  107 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7493 (t-90)
REVERT: A  159 MET cc_start: 0.8354 (ttp) cc_final: 0.7988 (tmm)
REVERT: A  295 MET cc_start: 0.8036 (ttm) cc_final: 0.7679 (ttm)
REVERT: A  450 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9138 (mm)
REVERT: A  458 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.8075 (m-80)
REVERT: A  487 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8561 (mm-40)
REVERT: A  495 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8730 (mm)
REVERT: A  517 ARG cc_start: 0.9048 (ttt180) cc_final: 0.8801 (ptp90)
REVERT: B  100 MET cc_start: 0.8910 (mmp) cc_final: 0.8672 (tpp)
REVERT: B  107 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8065 (t-90)
REVERT: B  133 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7652 (tm-30)
REVERT: B  149 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7694 (mm-30)
REVERT: B  276 MET cc_start: 0.7404 (mmp) cc_final: 0.6959 (mmt)
REVERT: B  481 LEU cc_start: 0.8613 (mm) cc_final: 0.8198 (mt)
REVERT: B  486 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8717 (mtt90)
  outliers start: 58
  outliers final: 44
  residues processed: 181
  average time/residue: 0.1873
  time to fit residues: 49.0197
Evaluate side-chains
  193 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 140
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  576 HIS
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 87 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 468 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.099201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.076565 restraints weight = 29380.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.078896 restraints weight = 16407.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.080437 restraints weight = 11101.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8950  Z= 0.131
  Angle     :  0.666  12.164  12092  Z= 0.329
  Chirality :  0.041   0.177   1440
  Planarity :  0.004   0.040   1532
  Dihedral  :  4.723  48.107   1241
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.32 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 31.10 %
    Favored  : 63.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1134
  helix:  1.32 (0.19), residues: 724
  sheet: -2.00 (0.67), residues: 46
  loop : -1.56 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 165 
 HIS   0.016   0.002   HIS A 214 
 PHE   0.028   0.002   PHE A 349 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04130 (  557)
  hydrogen bonds       : angle       4.28224 ( 1650)
  covalent geometry    : bond        0.00288 ( 8950)
  covalent geometry    : angle       0.66587 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 145
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.6349 (mmt) cc_final: 0.5853 (mmt)
REVERT: A   98 MET cc_start: 0.8860 (tpp) cc_final: 0.8119 (tpp)
REVERT: A  107 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7471 (t-90)
REVERT: A  295 MET cc_start: 0.8003 (ttm) cc_final: 0.7665 (ttm)
REVERT: A  458 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.8046 (m-80)
REVERT: A  487 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8574 (tp40)
REVERT: A  495 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8683 (mm)
REVERT: A  517 ARG cc_start: 0.9043 (ttt180) cc_final: 0.8790 (ptp90)
REVERT: B  100 MET cc_start: 0.8843 (mmp) cc_final: 0.8622 (tpp)
REVERT: B  102 ARG cc_start: 0.8562 (ttm170) cc_final: 0.8275 (mtm-85)
REVERT: B  107 HIS cc_start: 0.8515 (OUTLIER) cc_final: 0.8008 (t-90)
REVERT: B  133 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7695 (tm-30)
REVERT: B  149 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7658 (mm-30)
REVERT: B  210 MET cc_start: 0.8736 (mmt) cc_final: 0.8495 (mmt)
REVERT: B  465 LYS cc_start: 0.8390 (pttt) cc_final: 0.7971 (pptt)
REVERT: B  468 ASN cc_start: 0.8461 (t0) cc_final: 0.7862 (t0)
REVERT: B  481 LEU cc_start: 0.8585 (mm) cc_final: 0.8084 (mt)
REVERT: B  486 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8561 (mtt90)
  outliers start: 50
  outliers final: 37
  residues processed: 180
  average time/residue: 0.1912
  time to fit residues: 49.1087
Evaluate side-chains
  187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 142
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 95 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   chunk 100 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
A 464 ASN
A 477 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.099610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.077218 restraints weight = 29334.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.079577 restraints weight = 16242.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.081185 restraints weight = 10923.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8950  Z= 0.132
  Angle     :  0.692  12.166  12092  Z= 0.338
  Chirality :  0.041   0.177   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  4.667  48.695   1241
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.32 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 32.33 %
    Favored  : 62.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1134
  helix:  1.34 (0.19), residues: 724
  sheet: -0.95 (0.76), residues: 34
  loop : -1.57 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  91 
 HIS   0.017   0.001   HIS A 214 
 PHE   0.013   0.001   PHE A  23 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04091 (  557)
  hydrogen bonds       : angle       4.26019 ( 1650)
  covalent geometry    : bond        0.00295 ( 8950)
  covalent geometry    : angle       0.69197 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 145
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.6322 (mmt) cc_final: 0.5822 (mmt)
REVERT: A   98 MET cc_start: 0.8841 (tpp) cc_final: 0.8096 (tpp)
REVERT: A  210 MET cc_start: 0.8824 (mmt) cc_final: 0.8383 (tpp)
REVERT: A  295 MET cc_start: 0.7985 (ttm) cc_final: 0.7649 (ttm)
REVERT: A  465 LYS cc_start: 0.8243 (pttm) cc_final: 0.7305 (ptpt)
REVERT: A  487 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8565 (tp40)
REVERT: A  495 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8681 (mm)
REVERT: A  517 ARG cc_start: 0.9011 (ttt180) cc_final: 0.8785 (ptp90)
REVERT: B  100 MET cc_start: 0.8848 (mmp) cc_final: 0.8634 (tpp)
REVERT: B  102 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8285 (mtm-85)
REVERT: B  107 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7987 (t-90)
REVERT: B  133 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7676 (tm-30)
REVERT: B  149 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7692 (mm-30)
REVERT: B  160 MET cc_start: 0.8091 (tpp) cc_final: 0.7824 (tpp)
REVERT: B  210 MET cc_start: 0.8744 (mmt) cc_final: 0.8499 (mmt)
REVERT: B  276 MET cc_start: 0.7298 (mmp) cc_final: 0.6996 (mmt)
REVERT: B  374 LEU cc_start: 0.9026 (mm) cc_final: 0.8560 (tp)
REVERT: B  465 LYS cc_start: 0.8397 (pttt) cc_final: 0.8018 (pptt)
REVERT: B  468 ASN cc_start: 0.8419 (t0) cc_final: 0.7831 (t0)
REVERT: B  481 LEU cc_start: 0.8572 (mm) cc_final: 0.8064 (mt)
REVERT: B  486 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8565 (mtt90)
  outliers start: 46
  outliers final: 39
  residues processed: 176
  average time/residue: 0.1847
  time to fit residues: 46.2994
Evaluate side-chains
  189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 144
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0470
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.6878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.077468 restraints weight = 29609.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.079807 restraints weight = 16525.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.081407 restraints weight = 11180.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8950  Z= 0.129
  Angle     :  0.696  13.625  12092  Z= 0.337
  Chirality :  0.041   0.169   1440
  Planarity :  0.004   0.041   1532
  Dihedral  :  4.647  48.650   1241
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.32 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 31.92 %
    Favored  : 63.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.25), residues: 1134
  helix:  1.36 (0.19), residues: 724
  sheet: -0.89 (0.76), residues: 34
  loop : -1.57 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  91 
 HIS   0.017   0.002   HIS A 214 
 PHE   0.012   0.001   PHE A  23 
 TYR   0.012   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  557)
  hydrogen bonds       : angle       4.23390 ( 1650)
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.69605 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3680.09 seconds
wall clock time: 66 minutes 11.07 seconds (3971.07 seconds total)