Starting phenix.real_space_refine
on Mon Jun  9 12:53:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xln_38454/06_2025/8xln_38454.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xln_38454/06_2025/8xln_38454.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xln_38454/06_2025/8xln_38454.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xln_38454/06_2025/8xln_38454.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xln_38454/06_2025/8xln_38454.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xln_38454/06_2025/8xln_38454.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic.
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      37      5.16       5
     C    4211      2.51       5
     N    1073      2.21       5
     O    1272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6593
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "D"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "A"
      Number of atoms: 1533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1533
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 13, 'TRANS': 179}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.03, per 1000 atoms: 0.76
  Number of scatterers: 6593
  At special positions: 0
  Unit cell: (75.375, 102.51, 110.55, 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      37     16.00
     O    1272      8.00
     N    1073      7.00
     C    4211      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " 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
  Links applied
    ALPHA1-3
      " BMA H   3 " - " MAN H   4 "
    ALPHA1-6
      " BMA H   3 " - " MAN H   5 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG D 701 " - " ASN D 322 "
      " NAG D 702 " - " ASN D 432 "
      " NAG E   1 " - " ASN D  53 "
      " NAG F   1 " - " ASN D 546 "
      " NAG G   1 " - " ASN D  90 "
      " NAG H   1 " - " ASN D 103 "
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 923.9 milliseconds
  

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 4 sheets defined
      54.6% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.827A  pdb=" N   HIS D  34 " --> pdb=" O   ASP D  30 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU D  39 " --> pdb=" O   GLU D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 80
    Processing helix  chain 'D' and resid 90 through 105
      removed outlier: 3.581A  pdb=" N   LYS D  94 " --> pdb=" O   ASN D  90 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLN D  96 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 129
    Processing helix  chain 'D' and resid 146 through 155
      removed outlier: 4.285A  pdb=" N   GLU D 150 " --> pdb=" O   PRO D 146 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   MET D 152 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 172
      removed outlier: 3.852A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 194
      removed outlier: 4.119A  pdb=" N   LEU D 179 " --> pdb=" O   GLN D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 219 through 252
      removed outlier: 4.449A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 275 through 279
    Processing helix  chain 'D' and resid 293 through 301
      removed outlier: 3.807A  pdb=" N   MET D 297 " --> pdb=" O   VAL D 293 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL D 298 " --> pdb=" O   THR D 294 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 318
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.692A  pdb=" N   GLY D 377 " --> pdb=" O   HIS D 373 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   HIS D 378 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 412
      removed outlier: 4.019A  pdb=" N   GLY D 405 " --> pdb=" O   HIS D 401 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 422
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 4.007A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 466
      removed outlier: 4.326A  pdb=" N   PHE D 452 " --> pdb=" O   GLY D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 485
      removed outlier: 3.756A  pdb=" N   VAL D 485 " --> pdb=" O   LYS D 481 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 3.852A  pdb=" N   THR D 519 " --> pdb=" O   TYR D 515 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 561
      removed outlier: 3.974A  pdb=" N   GLN D 552 " --> pdb=" O   THR D 548 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU D 560 " --> pdb=" O   ASN D 556 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   GLY D 561 " --> pdb=" O   MET D 557 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 599
      Proline residue:  D 590  - end of helix
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 4.074A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 3.776A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.688A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'A' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'D' and resid 347 through 350
      removed outlier: 3.774A  pdb=" N   ARG D 357 " --> pdb=" O   TRP D 349 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.605A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474

    300 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 2.11 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: 2079
        1.35 -     1.47: 1780
        1.47 -     1.59: 2860
        1.59 -     1.71: 0
        1.71 -     1.83: 58
  Bond restraints: 6777
  Sorted by residual:
  bond pdb=" C   HIS D 265 "
       pdb=" N   LEU D 266 "
    ideal  model  delta    sigma   weight residual
    1.334  1.311  0.024 1.52e-02 4.33e+03 2.43e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" C1  BMA H   3 "
       pdb=" C2  BMA H   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.18e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.14e+00
  ... (remaining 6772 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 8950
        1.67 -     3.34: 214
        3.34 -     5.00: 38
        5.00 -     6.67: 12
        6.67 -     8.34: 1
  Bond angle restraints: 9215
  Sorted by residual:
  angle pdb=" C   CYS D 133 "
        pdb=" CA  CYS D 133 "
        pdb=" CB  CYS D 133 "
      ideal   model   delta    sigma   weight residual
     110.42  116.59   -6.17 1.99e+00 2.53e-01 9.62e+00
  angle pdb=" C   ALA D 264 "
        pdb=" N   HIS D 265 "
        pdb=" CA  HIS D 265 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.54e+00
  angle pdb=" CA  LEU D 162 "
        pdb=" CB  LEU D 162 "
        pdb=" CG  LEU D 162 "
      ideal   model   delta    sigma   weight residual
     116.30  124.64   -8.34 3.50e+00 8.16e-02 5.68e+00
  angle pdb=" C   ALA D 384 "
        pdb=" N   TYR D 385 "
        pdb=" CA  TYR D 385 "
      ideal   model   delta    sigma   weight residual
     122.65  118.78    3.87 1.66e+00 3.63e-01 5.42e+00
  angle pdb=" C   GLN D 102 "
        pdb=" N   ASN D 103 "
        pdb=" CA  ASN D 103 "
      ideal   model   delta    sigma   weight residual
     122.31  117.77    4.54 2.00e+00 2.50e-01 5.15e+00
  ... (remaining 9210 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.62: 3821
       21.62 -    43.23: 293
       43.23 -    64.85: 42
       64.85 -    86.46: 29
       86.46 -   108.08: 11
  Dihedral angle restraints: 4196
    sinusoidal: 1876
      harmonic: 2320
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.25   89.25     1      1.00e+01 1.00e-02 9.47e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.32   85.32     1      1.00e+01 1.00e-02 8.82e+01
  dihedral pdb=" CA  ARG A 403 "
           pdb=" C   ARG A 403 "
           pdb=" N   GLY A 404 "
           pdb=" CA  GLY A 404 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.56   20.44     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 4193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 827
       0.054 -    0.107: 170
       0.107 -    0.161: 12
       0.161 -    0.215: 0
       0.215 -    0.268: 2
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C5  BMA H   3 "
            pdb=" C4  BMA H   3 "
            pdb=" C6  BMA H   3 "
            pdb=" O5  BMA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ASN D 103 "
            pdb=" N   ASN D 103 "
            pdb=" C   ASN D 103 "
            pdb=" CB  ASN D 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.25e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 234 "    0.040 5.00e-02 4.00e+02   6.09e-02 5.93e+00
        pdb=" N   PRO D 235 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO D 235 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 235 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 145 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO D 146 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO D 146 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D 146 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 103 "    0.020 2.00e-02 2.50e+03   1.94e-02 4.69e+00
        pdb=" CG  ASN D 103 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 103 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 103 "   -0.014 2.00e-02 2.50e+03
        pdb=" C1  NAG H   1 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 201
        2.71 -     3.26: 6861
        3.26 -     3.80: 10402
        3.80 -     4.35: 12276
        4.35 -     4.90: 21018
  Nonbonded interactions: 50758
  Sorted by model distance:
  nonbonded pdb=" O   ILE D 151 "
            pdb=" OG  SER D 155 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OG  SER D 317 "
            pdb=" O   SER D 545 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ASN A 334 "
            pdb=" N   VAL A 362 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   PHE D 327 "
            pdb=" OG  SER D 331 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   MET D 152 "
            pdb=" NH2 ARG D 161 "
     model   vdw
     2.355 3.120
  ... (remaining 50753 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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:             3.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.030
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
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   0.039   6799  Z= 0.176
  Angle     :  0.662   8.339   9274  Z= 0.320
  Chirality :  0.043   0.268   1011
  Planarity :  0.005   0.061   1171
  Dihedral  : 17.143 108.077   2685
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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:  0.46 (0.31), residues: 785
  helix:  1.78 (0.27), residues: 377
  sheet:  0.15 (0.80), residues: 50
  loop : -1.34 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 477 
 HIS   0.005   0.001   HIS D 265 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.027   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00458 (    7)
  link_NAG-ASN         : angle       2.40818 (   21)
  link_ALPHA1-6        : bond        0.00373 (    1)
  link_ALPHA1-6        : angle       1.46731 (    3)
  link_BETA1-4         : bond        0.00516 (    6)
  link_BETA1-4         : angle       1.53806 (   18)
  link_ALPHA1-3        : bond        0.00377 (    1)
  link_ALPHA1-3        : angle       1.77605 (    3)
  hydrogen bonds       : bond        0.14482 (  300)
  hydrogen bonds       : angle       4.97075 (  846)
  SS BOND              : bond        0.00262 (    7)
  SS BOND              : angle       1.35150 (   14)
  covalent geometry    : bond        0.00369 ( 6777)
  covalent geometry    : angle       0.64676 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  194 ASN cc_start: 0.7537 (m-40) cc_final: 0.7149 (m110)
REVERT: D  270 MET cc_start: 0.8346 (tpp) cc_final: 0.7723 (tpp)
REVERT: A  467 ASP cc_start: 0.6564 (m-30) cc_final: 0.6347 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2016
  time to fit residues: 23.3408
Evaluate side-chains
  51 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0010
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
D  51 ASN
D  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.107270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.086135 restraints weight = 17295.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.088395 restraints weight = 9791.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.090039 restraints weight = 6941.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6799  Z= 0.128
  Angle     :  0.624  10.218   9274  Z= 0.307
  Chirality :  0.041   0.153   1011
  Planarity :  0.005   0.051   1171
  Dihedral  :  9.788  73.927   1163
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  7.94 %
    Favored  : 91.34 %
  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:  0.46 (0.30), residues: 785
  helix:  1.79 (0.26), residues: 375
  sheet: -0.39 (0.72), residues: 54
  loop : -1.25 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.014   0.001   PHE A 400 
 TYR   0.030   0.001   TYR D 385 
 ARG   0.005   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00462 (    7)
  link_NAG-ASN         : angle       2.36042 (   21)
  link_ALPHA1-6        : bond        0.00466 (    1)
  link_ALPHA1-6        : angle       2.32119 (    3)
  link_BETA1-4         : bond        0.00462 (    6)
  link_BETA1-4         : angle       1.80650 (   18)
  link_ALPHA1-3        : bond        0.00900 (    1)
  link_ALPHA1-3        : angle       2.41445 (    3)
  hydrogen bonds       : bond        0.04520 (  300)
  hydrogen bonds       : angle       4.40830 (  846)
  SS BOND              : bond        0.01250 (    7)
  SS BOND              : angle       2.66287 (   14)
  covalent geometry    : bond        0.00282 ( 6777)
  covalent geometry    : angle       0.59847 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  249 MET cc_start: 0.8286 (tpp) cc_final: 0.7905 (ttt)
REVERT: D  270 MET cc_start: 0.8070 (tpp) cc_final: 0.7664 (tpp)
REVERT: A  467 ASP cc_start: 0.6546 (m-30) cc_final: 0.6325 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 65
  average time/residue: 0.1697
  time to fit residues: 15.7383
Evaluate side-chains
  56 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain A residue  405 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 60 optimal weight:    0.3980
   chunk 7 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  49 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.107461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.085981 restraints weight = 17785.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.088360 restraints weight = 10178.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.089959 restraints weight = 7153.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6799  Z= 0.120
  Angle     :  0.579   8.253   9274  Z= 0.285
  Chirality :  0.041   0.172   1011
  Planarity :  0.004   0.053   1171
  Dihedral  :  7.934  63.869   1163
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.53 %
    Favored  : 88.31 %
  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:  0.43 (0.31), residues: 785
  helix:  1.86 (0.27), residues: 375
  sheet: -0.13 (0.73), residues: 54
  loop : -1.44 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 477 
 HIS   0.002   0.001   HIS D 374 
 PHE   0.010   0.001   PHE D 369 
 TYR   0.021   0.001   TYR D 385 
 ARG   0.004   0.000   ARG D 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    7)
  link_NAG-ASN         : angle       2.26223 (   21)
  link_ALPHA1-6        : bond        0.00728 (    1)
  link_ALPHA1-6        : angle       2.37616 (    3)
  link_BETA1-4         : bond        0.00386 (    6)
  link_BETA1-4         : angle       1.72800 (   18)
  link_ALPHA1-3        : bond        0.01139 (    1)
  link_ALPHA1-3        : angle       1.52209 (    3)
  hydrogen bonds       : bond        0.04183 (  300)
  hydrogen bonds       : angle       4.31822 (  846)
  SS BOND              : bond        0.00354 (    7)
  SS BOND              : angle       1.86733 (   14)
  covalent geometry    : bond        0.00265 ( 6777)
  covalent geometry    : angle       0.55847 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  270 MET cc_start: 0.8067 (tpp) cc_final: 0.7604 (tpp)
REVERT: A  391 CYS cc_start: 0.4445 (p) cc_final: 0.3641 (p)
REVERT: A  467 ASP cc_start: 0.6558 (m-30) cc_final: 0.6333 (m-30)
  outliers start: 8
  outliers final: 5
  residues processed: 70
  average time/residue: 0.1468
  time to fit residues: 15.0137
Evaluate side-chains
  60 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** 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 = 0.3553 r_free = 0.3553 target = 0.104528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.082876 restraints weight = 17770.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.085218 restraints weight = 10106.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.086665 restraints weight = 7091.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   6799  Z= 0.167
  Angle     :  0.633  14.181   9274  Z= 0.316
  Chirality :  0.042   0.280   1011
  Planarity :  0.005   0.050   1171
  Dihedral  :  7.557  58.351   1163
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.42 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.31), residues: 785
  helix:  1.81 (0.27), residues: 375
  sheet:  0.72 (0.86), residues: 42
  loop : -1.55 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 378 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.021   0.001   TYR A 380 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (    7)
  link_NAG-ASN         : angle       2.43837 (   21)
  link_ALPHA1-6        : bond        0.00707 (    1)
  link_ALPHA1-6        : angle       2.57333 (    3)
  link_BETA1-4         : bond        0.00332 (    6)
  link_BETA1-4         : angle       1.59197 (   18)
  link_ALPHA1-3        : bond        0.01168 (    1)
  link_ALPHA1-3        : angle       1.60126 (    3)
  hydrogen bonds       : bond        0.04644 (  300)
  hydrogen bonds       : angle       4.44620 (  846)
  SS BOND              : bond        0.00554 (    7)
  SS BOND              : angle       3.58300 (   14)
  covalent geometry    : bond        0.00388 ( 6777)
  covalent geometry    : angle       0.60222 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1575
  time to fit residues: 15.5367
Evaluate side-chains
  62 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  455 MET
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 69 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0980
   chunk 5 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.082814 restraints weight = 17742.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.085112 restraints weight = 10325.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.086655 restraints weight = 7341.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   6799  Z= 0.150
  Angle     :  0.617  14.416   9274  Z= 0.306
  Chirality :  0.041   0.215   1011
  Planarity :  0.004   0.052   1171
  Dihedral  :  6.714  49.964   1163
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.45 %
    Favored  : 82.25 %
  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:  0.30 (0.31), residues: 785
  helix:  1.77 (0.27), residues: 375
  sheet: -0.05 (0.76), residues: 52
  loop : -1.55 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 239 
 PHE   0.012   0.001   PHE D 369 
 TYR   0.016   0.001   TYR D 385 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00350 (    7)
  link_NAG-ASN         : angle       2.34138 (   21)
  link_ALPHA1-6        : bond        0.00772 (    1)
  link_ALPHA1-6        : angle       1.66935 (    3)
  link_BETA1-4         : bond        0.00334 (    6)
  link_BETA1-4         : angle       1.48169 (   18)
  link_ALPHA1-3        : bond        0.01171 (    1)
  link_ALPHA1-3        : angle       1.70867 (    3)
  hydrogen bonds       : bond        0.04597 (  300)
  hydrogen bonds       : angle       4.45589 (  846)
  SS BOND              : bond        0.00734 (    7)
  SS BOND              : angle       2.82116 (   14)
  covalent geometry    : bond        0.00347 ( 6777)
  covalent geometry    : angle       0.59415 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  332 MET cc_start: 0.9037 (tpt) cc_final: 0.8721 (tpt)
  outliers start: 9
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1512
  time to fit residues: 14.3996
Evaluate side-chains
  63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  455 MET
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.3565 r_free = 0.3565 target = 0.105251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.083858 restraints weight = 17497.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.086137 restraints weight = 10033.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.087727 restraints weight = 7098.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6799  Z= 0.127
  Angle     :  0.604  13.870   9274  Z= 0.298
  Chirality :  0.040   0.192   1011
  Planarity :  0.004   0.052   1171
  Dihedral  :  5.839  40.110   1163
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 16.88 %
    Favored  : 81.53 %
  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:  0.35 (0.31), residues: 785
  helix:  1.86 (0.27), residues: 373
  sheet: -0.68 (0.70), residues: 60
  loop : -1.47 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.010   0.001   PHE D 369 
 TYR   0.015   0.001   TYR D 385 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    7)
  link_NAG-ASN         : angle       2.18623 (   21)
  link_ALPHA1-6        : bond        0.00855 (    1)
  link_ALPHA1-6        : angle       1.55585 (    3)
  link_BETA1-4         : bond        0.00393 (    6)
  link_BETA1-4         : angle       1.50334 (   18)
  link_ALPHA1-3        : bond        0.01025 (    1)
  link_ALPHA1-3        : angle       2.09108 (    3)
  hydrogen bonds       : bond        0.04242 (  300)
  hydrogen bonds       : angle       4.36043 (  846)
  SS BOND              : bond        0.00824 (    7)
  SS BOND              : angle       2.79973 (   14)
  covalent geometry    : bond        0.00294 ( 6777)
  covalent geometry    : angle       0.58151 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  182 GLU cc_start: 0.8035 (tt0) cc_final: 0.7818 (tt0)
REVERT: D  239 HIS cc_start: 0.7964 (t70) cc_final: 0.7696 (t70)
REVERT: D  332 MET cc_start: 0.9025 (tpt) cc_final: 0.8694 (tpt)
  outliers start: 11
  outliers final: 10
  residues processed: 72
  average time/residue: 0.1519
  time to fit residues: 16.1414
Evaluate side-chains
  67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  455 MET
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    0.0040
   chunk 0 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.3563 r_free = 0.3563 target = 0.105078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.083335 restraints weight = 17659.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.085642 restraints weight = 10264.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.087208 restraints weight = 7301.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6799  Z= 0.136
  Angle     :  0.623  13.328   9274  Z= 0.307
  Chirality :  0.040   0.194   1011
  Planarity :  0.004   0.049   1171
  Dihedral  :  5.774  37.541   1163
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.17 %
    Favored  : 80.52 %
  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:  0.35 (0.31), residues: 785
  helix:  1.89 (0.27), residues: 372
  sheet: -0.64 (0.72), residues: 60
  loop : -1.49 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 378 
 PHE   0.015   0.001   PHE A 400 
 TYR   0.022   0.001   TYR D 385 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    7)
  link_NAG-ASN         : angle       2.19707 (   21)
  link_ALPHA1-6        : bond        0.00720 (    1)
  link_ALPHA1-6        : angle       1.44800 (    3)
  link_BETA1-4         : bond        0.00370 (    6)
  link_BETA1-4         : angle       1.52691 (   18)
  link_ALPHA1-3        : bond        0.01077 (    1)
  link_ALPHA1-3        : angle       1.69800 (    3)
  hydrogen bonds       : bond        0.04297 (  300)
  hydrogen bonds       : angle       4.31319 (  846)
  SS BOND              : bond        0.00707 (    7)
  SS BOND              : angle       2.92410 (   14)
  covalent geometry    : bond        0.00313 ( 6777)
  covalent geometry    : angle       0.60049 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  182 GLU cc_start: 0.7963 (tt0) cc_final: 0.7731 (tt0)
REVERT: D  239 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7674 (t70)
REVERT: D  249 MET cc_start: 0.8358 (tpp) cc_final: 0.8095 (mtm)
REVERT: D  332 MET cc_start: 0.9050 (tpt) cc_final: 0.8718 (tpt)
  outliers start: 16
  outliers final: 12
  residues processed: 72
  average time/residue: 0.1419
  time to fit residues: 15.2920
Evaluate side-chains
  70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  455 MET
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 70 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.3573 r_free = 0.3573 target = 0.105576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.083744 restraints weight = 17726.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.086085 restraints weight = 10324.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.087655 restraints weight = 7322.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6799  Z= 0.124
  Angle     :  0.605  12.943   9274  Z= 0.297
  Chirality :  0.040   0.200   1011
  Planarity :  0.004   0.050   1171
  Dihedral  :  5.430  35.731   1163
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.32 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.31), residues: 785
  helix:  1.77 (0.27), residues: 380
  sheet: -0.60 (0.72), residues: 59
  loop : -1.56 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.020   0.001   TYR D 385 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00336 (    7)
  link_NAG-ASN         : angle       2.06731 (   21)
  link_ALPHA1-6        : bond        0.00772 (    1)
  link_ALPHA1-6        : angle       1.56672 (    3)
  link_BETA1-4         : bond        0.00356 (    6)
  link_BETA1-4         : angle       1.56596 (   18)
  link_ALPHA1-3        : bond        0.00971 (    1)
  link_ALPHA1-3        : angle       1.56282 (    3)
  hydrogen bonds       : bond        0.04064 (  300)
  hydrogen bonds       : angle       4.24930 (  846)
  SS BOND              : bond        0.00791 (    7)
  SS BOND              : angle       2.67327 (   14)
  covalent geometry    : bond        0.00284 ( 6777)
  covalent geometry    : angle       0.58445 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  182 GLU cc_start: 0.7960 (tt0) cc_final: 0.7705 (tt0)
REVERT: D  239 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7636 (t70)
REVERT: D  249 MET cc_start: 0.8334 (tpp) cc_final: 0.8066 (mtm)
REVERT: D  332 MET cc_start: 0.9058 (tpt) cc_final: 0.8755 (tpt)
  outliers start: 13
  outliers final: 11
  residues processed: 73
  average time/residue: 0.1530
  time to fit residues: 16.1856
Evaluate side-chains
  71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  455 MET
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    0.4980
   chunk 59 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0020
   chunk 36 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.3605 r_free = 0.3605 target = 0.107462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.085607 restraints weight = 17659.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.087990 restraints weight = 9992.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.089640 restraints weight = 7058.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058   6799  Z= 0.109
  Angle     :  0.601  12.729   9274  Z= 0.291
  Chirality :  0.040   0.195   1011
  Planarity :  0.004   0.056   1171
  Dihedral  :  5.000  33.480   1163
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 18.04 %
    Favored  : 80.38 %
  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 (0.31), residues: 785
  helix:  1.89 (0.27), residues: 375
  sheet: -0.18 (0.80), residues: 49
  loop : -1.52 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.021   0.001   TYR D 385 
 ARG   0.001   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00354 (    7)
  link_NAG-ASN         : angle       1.84544 (   21)
  link_ALPHA1-6        : bond        0.00838 (    1)
  link_ALPHA1-6        : angle       1.56322 (    3)
  link_BETA1-4         : bond        0.00420 (    6)
  link_BETA1-4         : angle       1.60137 (   18)
  link_ALPHA1-3        : bond        0.00934 (    1)
  link_ALPHA1-3        : angle       1.56112 (    3)
  hydrogen bonds       : bond        0.03637 (  300)
  hydrogen bonds       : angle       4.13565 (  846)
  SS BOND              : bond        0.00601 (    7)
  SS BOND              : angle       2.31909 (   14)
  covalent geometry    : bond        0.00242 ( 6777)
  covalent geometry    : angle       0.58414 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  171 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8449 (mm-30)
REVERT: D  182 GLU cc_start: 0.7995 (tt0) cc_final: 0.7749 (tt0)
REVERT: D  239 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7619 (t70)
REVERT: D  249 MET cc_start: 0.8309 (tpp) cc_final: 0.8029 (mtm)
REVERT: D  270 MET cc_start: 0.7721 (tpt) cc_final: 0.7434 (tpp)
REVERT: D  332 MET cc_start: 0.8900 (tpt) cc_final: 0.8570 (tpt)
  outliers start: 11
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1529
  time to fit residues: 15.5510
Evaluate side-chains
  71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  379 ILE
Chi-restraints excluded: chain D residue  455 MET
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 71 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** D 300 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 = 0.3569 r_free = 0.3569 target = 0.105201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.083596 restraints weight = 17609.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.085904 restraints weight = 10090.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.087433 restraints weight = 7128.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6799  Z= 0.135
  Angle     :  0.610  12.634   9274  Z= 0.299
  Chirality :  0.040   0.192   1011
  Planarity :  0.004   0.049   1171
  Dihedral  :  5.119  34.383   1163
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.46 %
    Favored  : 80.66 %
  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:  0.46 (0.31), residues: 785
  helix:  2.05 (0.27), residues: 366
  sheet: -0.40 (0.79), residues: 50
  loop : -1.49 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 378 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.020   0.001   TYR D 385 
 ARG   0.002   0.000   ARG D 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00343 (    7)
  link_NAG-ASN         : angle       2.08458 (   21)
  link_ALPHA1-6        : bond        0.00684 (    1)
  link_ALPHA1-6        : angle       1.57466 (    3)
  link_BETA1-4         : bond        0.00345 (    6)
  link_BETA1-4         : angle       1.57975 (   18)
  link_ALPHA1-3        : bond        0.00890 (    1)
  link_ALPHA1-3        : angle       1.37859 (    3)
  hydrogen bonds       : bond        0.04155 (  300)
  hydrogen bonds       : angle       4.23094 (  846)
  SS BOND              : bond        0.00772 (    7)
  SS BOND              : angle       2.39977 (   14)
  covalent geometry    : bond        0.00312 ( 6777)
  covalent geometry    : angle       0.59161 ( 9215)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  182 GLU cc_start: 0.8024 (tt0) cc_final: 0.7782 (tt0)
REVERT: D  239 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7620 (t70)
REVERT: D  249 MET cc_start: 0.8312 (tpp) cc_final: 0.8107 (mtm)
REVERT: D  270 MET cc_start: 0.7700 (tpt) cc_final: 0.7085 (tpp)
REVERT: D  332 MET cc_start: 0.9062 (tpt) cc_final: 0.8793 (tpt)
  outliers start: 13
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1450
  time to fit residues: 14.6486
Evaluate side-chains
  70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  455 MET
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0170
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.9224

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

Flipped N/Q/H residues before XYZ refinement:
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 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 = 0.3571 r_free = 0.3571 target = 0.105274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.083530 restraints weight = 17871.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.085834 restraints weight = 10283.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.087397 restraints weight = 7284.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6799  Z= 0.129
  Angle     :  0.608  12.533   9274  Z= 0.297
  Chirality :  0.040   0.183   1011
  Planarity :  0.004   0.049   1171
  Dihedral  :  5.068  33.996   1163
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.89 %
    Favored  : 80.52 %
  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 (0.31), residues: 785
  helix:  2.00 (0.27), residues: 367
  sheet: -0.90 (0.70), residues: 60
  loop : -1.45 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D 265 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.019   0.001   TYR D 385 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00331 (    7)
  link_NAG-ASN         : angle       2.03486 (   21)
  link_ALPHA1-6        : bond        0.00643 (    1)
  link_ALPHA1-6        : angle       1.56252 (    3)
  link_BETA1-4         : bond        0.00362 (    6)
  link_BETA1-4         : angle       1.58839 (   18)
  link_ALPHA1-3        : bond        0.00859 (    1)
  link_ALPHA1-3        : angle       1.36807 (    3)
  hydrogen bonds       : bond        0.04133 (  300)
  hydrogen bonds       : angle       4.23913 (  846)
  SS BOND              : bond        0.00651 (    7)
  SS BOND              : angle       2.35449 (   14)
  covalent geometry    : bond        0.00299 ( 6777)
  covalent geometry    : angle       0.59017 ( 9215)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2240.56 seconds
wall clock time: 39 minutes 39.03 seconds (2379.03 seconds total)