Starting phenix.real_space_refine
on Fri Aug 22 18:22:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx2_37898/08_2025/8wx2_37898.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx2_37898/08_2025/8wx2_37898.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx2_37898/08_2025/8wx2_37898.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx2_37898/08_2025/8wx2_37898.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx2_37898/08_2025/8wx2_37898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx2_37898/08_2025/8wx2_37898.map"
  }
  resolution = 3.44
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.047
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      36      5.16       5
     C    4528      2.51       5
     N    1110      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6800
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3400
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 23, 'TRANS': 416}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 24
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.89, per 1000 atoms: 0.28
  Number of scatterers: 6800
  At special positions: 0
  Unit cell: (128.65, 88.81, 81.34, 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      36     16.00
     O    1126      8.00
     N    1110      7.00
     C    4528      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 526 " - pdb=" SG  CYS A 536 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 526 " - pdb=" SG  CYS B 536 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 359.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      86.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 63
    Processing helix  chain 'A' and resid 67 through 71
      removed outlier: 3.913A  pdb=" N   GLN A  71 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 98
      removed outlier: 3.555A  pdb=" N   VAL A  78 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 100 through 123
      removed outlier: 3.601A  pdb=" N   VAL A 104 " --> pdb=" O   ARG A 100 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 123 through 131
      removed outlier: 3.730A  pdb=" N   ARG A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 191
    Processing helix  chain 'A' and resid 191 through 224
      removed outlier: 3.774A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 247
      Proline residue:  A 233  - end of helix
    Processing helix  chain 'A' and resid 304 through 322
      removed outlier: 3.700A  pdb=" N   PHE A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN A 311 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 312 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS A 315 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      Proline residue:  A 318  - end of helix
    Processing helix  chain 'A' and resid 322 through 343
      removed outlier: 3.826A  pdb=" N   TYR A 326 " --> pdb=" O   THR A 322 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLN A 332 " --> pdb=" O   MET A 328 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 333 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL A 338 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 393
      removed outlier: 3.811A  pdb=" N   LEU A 375 " --> pdb=" O   PRO A 371 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   LEU A 376 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL A 380 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 387 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
      Proline residue:  A 388  - end of helix
    Processing helix  chain 'A' and resid 393 through 401
      removed outlier: 3.537A  pdb=" N   LEU A 399 " --> pdb=" O   ASP A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 439
      removed outlier: 3.643A  pdb=" N   TYR A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 436 " --> pdb=" O   ARG A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 460
    Processing helix  chain 'A' and resid 461 through 474
    Processing helix  chain 'A' and resid 476 through 484
    Processing helix  chain 'A' and resid 491 through 517
      removed outlier: 3.765A  pdb=" N   MET A 496 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER A 503 " --> pdb=" O   PHE A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 532
    Processing helix  chain 'A' and resid 537 through 564
      removed outlier: 3.541A  pdb=" N   GLU A 564 " --> pdb=" O   ALA A 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 63
    Processing helix  chain 'B' and resid 67 through 71
      removed outlier: 3.913A  pdb=" N   GLN B  71 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 98
      removed outlier: 3.555A  pdb=" N   VAL B  78 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 100 through 123
      removed outlier: 3.602A  pdb=" N   VAL B 104 " --> pdb=" O   ARG B 100 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 123 through 131
      removed outlier: 3.730A  pdb=" N   ARG B 127 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 191
    Processing helix  chain 'B' and resid 191 through 224
      removed outlier: 3.774A  pdb=" N   ILE B 224 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 247
      Proline residue:  B 233  - end of helix
    Processing helix  chain 'B' and resid 304 through 322
      removed outlier: 3.700A  pdb=" N   PHE B 310 " --> pdb=" O   ASP B 306 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN B 311 " --> pdb=" O   ILE B 307 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL B 312 " --> pdb=" O   ALA B 308 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS B 315 " --> pdb=" O   GLN B 311 " (cutoff:3.500A)
      Proline residue:  B 318  - end of helix
    Processing helix  chain 'B' and resid 322 through 343
      removed outlier: 3.827A  pdb=" N   TYR B 326 " --> pdb=" O   THR B 322 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLN B 332 " --> pdb=" O   MET B 328 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   MET B 333 " --> pdb=" O   VAL B 329 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 335 " --> pdb=" O   PHE B 331 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL B 338 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 393
      removed outlier: 3.811A  pdb=" N   LEU B 375 " --> pdb=" O   PRO B 371 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   LEU B 376 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL B 383 " --> pdb=" O   ASN B 379 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL B 387 " --> pdb=" O   VAL B 383 " (cutoff:3.500A)
      Proline residue:  B 388  - end of helix
    Processing helix  chain 'B' and resid 393 through 401
      removed outlier: 3.537A  pdb=" N   LEU B 399 " --> pdb=" O   ASP B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 439
      removed outlier: 3.644A  pdb=" N   TYR B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE B 436 " --> pdb=" O   ARG B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 460
    Processing helix  chain 'B' and resid 461 through 474
    Processing helix  chain 'B' and resid 476 through 484
    Processing helix  chain 'B' and resid 491 through 517
      removed outlier: 3.764A  pdb=" N   MET B 496 " --> pdb=" O   GLN B 492 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER B 503 " --> pdb=" O   PHE B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 532
    Processing helix  chain 'B' and resid 537 through 564
      removed outlier: 3.540A  pdb=" N   GLU B 564 " --> pdb=" O   ALA B 560 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1566 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.87

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2080
        1.35 -     1.47: 1782
        1.47 -     1.59: 3062
        1.59 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6982
  Sorted by residual:
  bond pdb=" C   ALA A 487 "
       pdb=" N   PRO A 488 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.036 2.34e-02 1.83e+03 2.31e+00
  bond pdb=" C   ALA B 487 "
       pdb=" N   PRO B 488 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.17e+00
  bond pdb=" C   LEU B 519 "
       pdb=" N   PRO B 520 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 7.99e-01
  bond pdb=" C   LEU A 519 "
       pdb=" N   PRO A 520 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.36e-01
  bond pdb=" CA  THR B 248 "
       pdb=" C   THR B 248 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.63e-01
  ... (remaining 6977 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 9274
        1.57 -     3.14: 162
        3.14 -     4.70: 55
        4.70 -     6.27: 19
        6.27 -     7.84: 12
  Bond angle restraints: 9522
  Sorted by residual:
  angle pdb=" N   PRO A 351 "
        pdb=" CA  PRO A 351 "
        pdb=" CB  PRO A 351 "
      ideal   model   delta    sigma   weight residual
     103.00  110.44   -7.44 1.10e+00 8.26e-01 4.58e+01
  angle pdb=" N   PRO B 351 "
        pdb=" CA  PRO B 351 "
        pdb=" CB  PRO B 351 "
      ideal   model   delta    sigma   weight residual
     103.00  110.41   -7.41 1.10e+00 8.26e-01 4.53e+01
  angle pdb=" N   ALA A 487 "
        pdb=" CA  ALA A 487 "
        pdb=" C   ALA A 487 "
      ideal   model   delta    sigma   weight residual
     109.81  117.65   -7.84 2.21e+00 2.05e-01 1.26e+01
  angle pdb=" N   ALA B 487 "
        pdb=" CA  ALA B 487 "
        pdb=" C   ALA B 487 "
      ideal   model   delta    sigma   weight residual
     109.81  117.60   -7.79 2.21e+00 2.05e-01 1.24e+01
  angle pdb=" N   ARG B  74 "
        pdb=" CA  ARG B  74 "
        pdb=" CB  ARG B  74 "
      ideal   model   delta    sigma   weight residual
     114.17  110.48    3.69 1.14e+00 7.69e-01 1.05e+01
  ... (remaining 9517 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.95: 3528
       14.95 -    29.91: 338
       29.91 -    44.86: 128
       44.86 -    59.81: 38
       59.81 -    74.77: 4
  Dihedral angle restraints: 4036
    sinusoidal: 1510
      harmonic: 2526
  Sorted by residual:
  dihedral pdb=" CA  ALA B 487 "
           pdb=" C   ALA B 487 "
           pdb=" N   PRO B 488 "
           pdb=" CA  PRO B 488 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.20  -44.80     0      5.00e+00 4.00e-02 8.03e+01
  dihedral pdb=" CA  ALA A 487 "
           pdb=" C   ALA A 487 "
           pdb=" N   PRO A 488 "
           pdb=" CA  PRO A 488 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.27  -44.73     0      5.00e+00 4.00e-02 8.00e+01
  dihedral pdb=" CB  CYS B 131 "
           pdb=" SG  CYS B 131 "
           pdb=" SG  CYS B 157 "
           pdb=" CB  CYS B 157 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -28.54  -57.46     1      1.00e+01 1.00e-02 4.44e+01
  ... (remaining 4033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 917
       0.049 -    0.098: 166
       0.098 -    0.147: 25
       0.147 -    0.196: 0
       0.196 -    0.245: 2
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CA  PRO B 351 "
            pdb=" N   PRO B 351 "
            pdb=" C   PRO B 351 "
            pdb=" CB  PRO B 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  PRO A 351 "
            pdb=" N   PRO A 351 "
            pdb=" C   PRO A 351 "
            pdb=" CB  PRO A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  PRO B 488 "
            pdb=" N   PRO B 488 "
            pdb=" C   PRO B 488 "
            pdb=" CB  PRO B 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.37e-01
  ... (remaining 1107 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 487 "    0.048 5.00e-02 4.00e+02   7.35e-02 8.64e+00
        pdb=" N   PRO A 488 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 488 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 488 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 487 "   -0.048 5.00e-02 4.00e+02   7.32e-02 8.57e+00
        pdb=" N   PRO B 488 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 488 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 488 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 118 "    0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO B 119 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 119 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 119 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 184
        2.72 -     3.26: 7458
        3.26 -     3.81: 11484
        3.81 -     4.35: 13588
        4.35 -     4.90: 22303
  Nonbonded interactions: 55017
  Sorted by model distance:
  nonbonded pdb=" N   ASN A  66 "
            pdb=" OD1 ASN A  66 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" N   ASN B  66 "
            pdb=" OD1 ASN B  66 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O   PHE B  65 "
            pdb=" N   THR B  68 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   PHE A  65 "
            pdb=" N   THR A  68 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   VAL B 514 "
            pdb=" OG  SER B 518 "
     model   vdw
     2.329 3.040
  ... (remaining 55012 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: 0.01
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 individual isotropic
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:             2.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.280
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
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      :  0.002   0.036   6986  Z= 0.124
  Angle     :  0.646   7.841   9530  Z= 0.357
  Chirality :  0.038   0.245   1110
  Planarity :  0.005   0.074   1172
  Dihedral  : 14.514  74.766   2400
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  6.51 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.25 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.26), residues: 860
  helix: -0.96 (0.18), residues: 680
  sheet:  None (None), residues: 0
  loop : -3.01 (0.47), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 489 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.011   0.001   PHE A  65 
 TRP   0.002   0.000   TRP A  67 
 HIS   0.001   0.000   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6982)
  covalent geometry    : angle       0.64602 ( 9522)
  SS BOND              : bond        0.00259 (    4)
  SS BOND              : angle       0.81986 (    8)
  hydrogen bonds       : bond        0.18655 (  532)
  hydrogen bonds       : angle       6.74385 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ARG cc_start: 0.5625 (mtm-85) cc_final: 0.5291 (mtp180)
REVERT: A  460 TRP cc_start: 0.5111 (m-90) cc_final: 0.4847 (m-10)
  outliers start: 14
  outliers final: 8
  residues processed: 169
  average time/residue: 0.0518
  time to fit residues: 12.1011
Evaluate side-chains
  116 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain B residue   66 ASN
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
A 343 HIS
A 437 HIS
B 178 ASN
B 343 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.163036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.140259 restraints weight = 17460.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.4277 rms_B_bonded: 3.00
r_work: 0.4137 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6986  Z= 0.178
  Angle     :  0.787  11.214   9530  Z= 0.384
  Chirality :  0.043   0.148   1110
  Planarity :  0.007   0.076   1172
  Dihedral  :  6.717  58.787    950
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 18.66 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.28), residues: 860
  helix:  0.20 (0.19), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.05 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 562 
 TYR   0.025   0.002   TYR A  59 
 PHE   0.026   0.002   PHE A 202 
 TRP   0.011   0.001   TRP B 558 
 HIS   0.007   0.002   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6982)
  covalent geometry    : angle       0.78670 ( 9522)
  SS BOND              : bond        0.00056 (    4)
  SS BOND              : angle       0.50474 (    8)
  hydrogen bonds       : bond        0.04521 (  532)
  hydrogen bonds       : angle       4.75106 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 PHE cc_start: 0.6641 (t80) cc_final: 0.6101 (t80)
REVERT: A  460 TRP cc_start: 0.5369 (m-90) cc_final: 0.4690 (m100)
REVERT: A  496 MET cc_start: 0.8016 (mmm) cc_final: 0.7750 (mmt)
REVERT: B  460 TRP cc_start: 0.5425 (m-90) cc_final: 0.5087 (m-10)
  outliers start: 29
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0579
  time to fit residues: 10.6731
Evaluate side-chains
  118 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain B residue   66 ASN
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0670
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.7118

-------------------------------------------------------------------------------
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 = 0.4578 r_free = 0.4578 target = 0.162717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.140057 restraints weight = 17499.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.4268 rms_B_bonded: 3.03
r_work: 0.4125 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6986  Z= 0.152
  Angle     :  0.750  10.408   9530  Z= 0.362
  Chirality :  0.041   0.148   1110
  Planarity :  0.006   0.079   1172
  Dihedral  :  6.510  58.199    948
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.94 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.29), residues: 860
  helix:  0.60 (0.19), residues: 718
  sheet:  None (None), residues: 0
  loop : -3.34 (0.50), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 537 
 TYR   0.016   0.001   TYR B  59 
 PHE   0.020   0.001   PHE A 244 
 TRP   0.007   0.001   TRP B 558 
 HIS   0.005   0.001   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6982)
  covalent geometry    : angle       0.74958 ( 9522)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       0.80228 (    8)
  hydrogen bonds       : bond        0.04428 (  532)
  hydrogen bonds       : angle       4.50754 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.3141 (OUTLIER) cc_final: -0.0048 (ttt180)
REVERT: A  101 TYR cc_start: 0.5792 (t80) cc_final: 0.5565 (t80)
REVERT: A  219 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6883 (m-80)
REVERT: A  460 TRP cc_start: 0.5421 (m-90) cc_final: 0.4760 (m100)
REVERT: A  486 GLU cc_start: 0.5353 (pm20) cc_final: 0.4912 (mp0)
REVERT: A  496 MET cc_start: 0.8027 (mmm) cc_final: 0.7805 (mmt)
REVERT: B   74 ARG cc_start: 0.3278 (OUTLIER) cc_final: -0.0117 (ttt180)
REVERT: B  198 PHE cc_start: 0.6595 (t80) cc_final: 0.6113 (t80)
REVERT: B  310 PHE cc_start: 0.8018 (m-10) cc_final: 0.7815 (m-10)
REVERT: B  460 TRP cc_start: 0.5360 (m-90) cc_final: 0.4656 (m100)
  outliers start: 33
  outliers final: 17
  residues processed: 121
  average time/residue: 0.0591
  time to fit residues: 10.0458
Evaluate side-chains
  115 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue   74 ARG
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  332 GLN
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 27 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0570
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    0.1980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.4579 r_free = 0.4579 target = 0.162738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.140386 restraints weight = 17439.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.4278 rms_B_bonded: 3.00
r_work: 0.4143 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6986  Z= 0.141
  Angle     :  0.742  12.107   9530  Z= 0.352
  Chirality :  0.041   0.192   1110
  Planarity :  0.005   0.076   1172
  Dihedral  :  6.124  59.995    946
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 20.09 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.29), residues: 860
  helix:  0.85 (0.19), residues: 722
  sheet:  None (None), residues: 0
  loop : -3.37 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 197 
 TYR   0.010   0.001   TYR A 484 
 PHE   0.018   0.001   PHE A 244 
 TRP   0.005   0.000   TRP A 558 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6982)
  covalent geometry    : angle       0.74235 ( 9522)
  SS BOND              : bond        0.00137 (    4)
  SS BOND              : angle       0.70803 (    8)
  hydrogen bonds       : bond        0.04064 (  532)
  hydrogen bonds       : angle       4.29631 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 102
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6844 (m-80)
REVERT: A  460 TRP cc_start: 0.5402 (m-90) cc_final: 0.4762 (m100)
REVERT: A  538 MET cc_start: 0.6599 (tpt) cc_final: 0.6294 (tpt)
REVERT: B   74 ARG cc_start: 0.3359 (OUTLIER) cc_final: -0.0047 (ttt180)
REVERT: B  460 TRP cc_start: 0.5343 (m-90) cc_final: 0.4655 (m100)
  outliers start: 36
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0479
  time to fit residues: 8.5809
Evaluate side-chains
  111 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  438 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0050
   chunk 72 optimal weight:    0.0070
   chunk 27 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   overall best weight:    0.4812

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.162785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.140121 restraints weight = 17524.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.4270 rms_B_bonded: 3.04
r_work: 0.4128 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6986  Z= 0.142
  Angle     :  0.757  12.368   9530  Z= 0.359
  Chirality :  0.042   0.180   1110
  Planarity :  0.006   0.075   1172
  Dihedral  :  5.705  44.839    942
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 21.37 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.30), residues: 860
  helix:  1.16 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -2.81 (0.50), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  74 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.018   0.001   PHE A 244 
 TRP   0.005   0.000   TRP A 558 
 HIS   0.002   0.000   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6982)
  covalent geometry    : angle       0.75039 ( 9522)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       3.48896 (    8)
  hydrogen bonds       : bond        0.04054 (  532)
  hydrogen bonds       : angle       4.22159 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.5738 (t80) cc_final: 0.5408 (t80)
REVERT: A  219 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6891 (m-80)
REVERT: A  460 TRP cc_start: 0.5458 (m-90) cc_final: 0.4760 (m100)
REVERT: A  538 MET cc_start: 0.6615 (tpt) cc_final: 0.6288 (tpt)
REVERT: B   74 ARG cc_start: 0.3164 (OUTLIER) cc_final: -0.0092 (ttt180)
REVERT: B  219 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6648 (m-80)
REVERT: B  460 TRP cc_start: 0.5350 (m-90) cc_final: 0.4655 (m100)
  outliers start: 33
  outliers final: 18
  residues processed: 126
  average time/residue: 0.0641
  time to fit residues: 11.3338
Evaluate side-chains
  115 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  332 GLN
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:   20.0000
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 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 = 0.4531 r_free = 0.4531 target = 0.158723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.135320 restraints weight = 17436.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.4207 rms_B_bonded: 2.98
r_work: 0.4063 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6986  Z= 0.173
  Angle     :  0.780  11.274   9530  Z= 0.377
  Chirality :  0.045   0.214   1110
  Planarity :  0.006   0.077   1172
  Dihedral  :  5.630  44.244    942
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 21.37 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.29), residues: 860
  helix:  1.00 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -3.98 (0.47), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  46 
 TYR   0.016   0.002   TYR A 484 
 PHE   0.021   0.001   PHE B 310 
 TRP   0.008   0.001   TRP A 558 
 HIS   0.002   0.000   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6982)
  covalent geometry    : angle       0.77769 ( 9522)
  SS BOND              : bond        0.00235 (    4)
  SS BOND              : angle       1.99321 (    8)
  hydrogen bonds       : bond        0.04397 (  532)
  hydrogen bonds       : angle       4.29737 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 98
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TRP cc_start: 0.5624 (m-90) cc_final: 0.5020 (m100)
REVERT: B   74 ARG cc_start: 0.3284 (OUTLIER) cc_final: -0.0041 (ttt180)
REVERT: B  460 TRP cc_start: 0.5692 (m-90) cc_final: 0.5003 (m100)
  outliers start: 35
  outliers final: 26
  residues processed: 124
  average time/residue: 0.0522
  time to fit residues: 9.4663
Evaluate side-chains
  120 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASN
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  332 GLN
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.0870
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0370
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0060
   chunk 57 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 70 optimal weight:    0.3980
   overall best weight:    0.1852

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 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 = 0.4566 r_free = 0.4566 target = 0.161600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.139113 restraints weight = 17242.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.4264 rms_B_bonded: 2.99
r_work: 0.4124 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6986  Z= 0.143
  Angle     :  0.774  13.730   9530  Z= 0.367
  Chirality :  0.044   0.280   1110
  Planarity :  0.005   0.075   1172
  Dihedral  :  5.513  43.785    942
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 23.08 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.30), residues: 860
  helix:  1.38 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.13 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  74 
 TYR   0.017   0.001   TYR A  59 
 PHE   0.021   0.001   PHE B 310 
 TRP   0.006   0.000   TRP B 204 
 HIS   0.004   0.000   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6982)
  covalent geometry    : angle       0.77303 ( 9522)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       1.43491 (    8)
  hydrogen bonds       : bond        0.03989 (  532)
  hydrogen bonds       : angle       4.17817 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.7176 (t80) cc_final: 0.6922 (t80)
REVERT: A  460 TRP cc_start: 0.5502 (m-90) cc_final: 0.4901 (m100)
REVERT: B   74 ARG cc_start: 0.3058 (OUTLIER) cc_final: 0.0041 (ttt180)
REVERT: B  219 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6621 (m-80)
REVERT: B  460 TRP cc_start: 0.5461 (m-90) cc_final: 0.4827 (m100)
  outliers start: 31
  outliers final: 25
  residues processed: 121
  average time/residue: 0.0515
  time to fit residues: 9.0451
Evaluate side-chains
  116 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  332 GLN
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 17 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0470
   chunk 36 optimal weight:    0.1980
   chunk 20 optimal weight:    0.0010
   chunk 54 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   overall best weight:    0.3684

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 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 = 0.4571 r_free = 0.4571 target = 0.161974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.139534 restraints weight = 17425.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.4267 rms_B_bonded: 2.98
r_work: 0.4130 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6986  Z= 0.143
  Angle     :  0.769  12.913   9530  Z= 0.366
  Chirality :  0.044   0.276   1110
  Planarity :  0.006   0.098   1172
  Dihedral  :  5.500  43.589    942
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 23.65 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.30), residues: 860
  helix:  1.53 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop : -3.05 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  74 
 TYR   0.011   0.001   TYR B 563 
 PHE   0.023   0.001   PHE B 310 
 TRP   0.005   0.000   TRP A 558 
 HIS   0.001   0.000   HIS A 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6982)
  covalent geometry    : angle       0.76880 ( 9522)
  SS BOND              : bond        0.00101 (    4)
  SS BOND              : angle       1.28161 (    8)
  hydrogen bonds       : bond        0.03920 (  532)
  hydrogen bonds       : angle       4.14900 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.7213 (t80) cc_final: 0.6971 (t80)
REVERT: A  460 TRP cc_start: 0.5472 (m-90) cc_final: 0.4888 (m100)
REVERT: B   74 ARG cc_start: 0.3398 (OUTLIER) cc_final: 0.0343 (ttt180)
REVERT: B  198 PHE cc_start: 0.6540 (t80) cc_final: 0.6147 (t80)
REVERT: B  219 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6592 (m-80)
REVERT: B  460 TRP cc_start: 0.5514 (m-90) cc_final: 0.4853 (m100)
  outliers start: 33
  outliers final: 29
  residues processed: 120
  average time/residue: 0.0488
  time to fit residues: 8.5165
Evaluate side-chains
  120 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  332 GLN
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0670
   chunk 64 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 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 = 0.4572 r_free = 0.4572 target = 0.161441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.138945 restraints weight = 17539.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.4266 rms_B_bonded: 3.02
r_work: 0.4125 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   6986  Z= 0.151
  Angle     :  0.789  13.527   9530  Z= 0.374
  Chirality :  0.045   0.271   1110
  Planarity :  0.006   0.099   1172
  Dihedral  :  5.519  44.447    942
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.36 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.30), residues: 860
  helix:  1.51 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop : -2.99 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  74 
 TYR   0.011   0.001   TYR B 563 
 PHE   0.025   0.001   PHE B 310 
 TRP   0.004   0.001   TRP A 558 
 HIS   0.001   0.000   HIS A 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6982)
  covalent geometry    : angle       0.78886 ( 9522)
  SS BOND              : bond        0.00059 (    4)
  SS BOND              : angle       1.23278 (    8)
  hydrogen bonds       : bond        0.03974 (  532)
  hydrogen bonds       : angle       4.18337 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.7279 (t80) cc_final: 0.7044 (t80)
REVERT: A  460 TRP cc_start: 0.5466 (m-90) cc_final: 0.4855 (m100)
REVERT: B   74 ARG cc_start: 0.3154 (OUTLIER) cc_final: 0.0282 (ttt180)
REVERT: B  219 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6662 (m-80)
REVERT: B  460 TRP cc_start: 0.5509 (m-90) cc_final: 0.4856 (m100)
  outliers start: 30
  outliers final: 28
  residues processed: 116
  average time/residue: 0.0544
  time to fit residues: 9.2363
Evaluate side-chains
  118 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  332 GLN
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:   30.0000
   chunk 50 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0980
   chunk 5 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0020
   chunk 28 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0370
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.3066

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 437 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.162610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.140885 restraints weight = 17551.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.4294 rms_B_bonded: 2.98
r_work: 0.4156 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6986  Z= 0.142
  Angle     :  0.777  14.171   9530  Z= 0.368
  Chirality :  0.044   0.265   1110
  Planarity :  0.006   0.094   1172
  Dihedral  :  5.447  43.536    942
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.08 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.30), residues: 860
  helix:  1.58 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.08 (0.46), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  74 
 TYR   0.011   0.001   TYR B 563 
 PHE   0.035   0.001   PHE B 202 
 TRP   0.006   0.001   TRP B 201 
 HIS   0.005   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6982)
  covalent geometry    : angle       0.77670 ( 9522)
  SS BOND              : bond        0.00114 (    4)
  SS BOND              : angle       1.20577 (    8)
  hydrogen bonds       : bond        0.03832 (  532)
  hydrogen bonds       : angle       4.14380 ( 1566)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.7203 (t80) cc_final: 0.6973 (t80)
REVERT: A  460 TRP cc_start: 0.5357 (m-90) cc_final: 0.4816 (m100)
REVERT: B   74 ARG cc_start: 0.3237 (OUTLIER) cc_final: 0.0339 (ttt180)
REVERT: B  198 PHE cc_start: 0.6360 (t80) cc_final: 0.5917 (t80)
REVERT: B  219 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6557 (m-80)
REVERT: B  460 TRP cc_start: 0.5406 (m-90) cc_final: 0.4797 (m100)
  outliers start: 30
  outliers final: 26
  residues processed: 122
  average time/residue: 0.0500
  time to fit residues: 8.7913
Evaluate side-chains
  117 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  111 TYR
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  542 PHE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  332 GLN
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  526 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0030
   chunk 26 optimal weight:    0.6980
   chunk 25 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.3908

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 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 = 0.4589 r_free = 0.4589 target = 0.162742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.140744 restraints weight = 17528.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.4290 rms_B_bonded: 3.02
r_work: 0.4153 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6986  Z= 0.145
  Angle     :  0.794  14.057   9530  Z= 0.374
  Chirality :  0.046   0.263   1110
  Planarity :  0.006   0.095   1172
  Dihedral  :  5.465  43.583    942
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.21 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.30), residues: 860
  helix:  1.55 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.05 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  74 
 TYR   0.016   0.001   TYR B 111 
 PHE   0.026   0.001   PHE B 310 
 TRP   0.006   0.001   TRP A 558 
 HIS   0.001   0.000   HIS A 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6982)
  covalent geometry    : angle       0.79321 ( 9522)
  SS BOND              : bond        0.00068 (    4)
  SS BOND              : angle       1.16218 (    8)
  hydrogen bonds       : bond        0.03853 (  532)
  hydrogen bonds       : angle       4.16914 ( 1566)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1361.14 seconds
wall clock time: 24 minutes 4.37 seconds (1444.37 seconds total)