Starting phenix.real_space_refine
on Tue Mar  3 14:28:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oix_12935/03_2026/7oix_12935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oix_12935/03_2026/7oix_12935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2026/7oix_12935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2026/7oix_12935.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2026/7oix_12935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oix_12935/03_2026/7oix_12935.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    3814      2.51       5
     N     937      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5869
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2097
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 21, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 3558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3558
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 21, 'TRANS': 429}
          Chain breaks: 1
    Chain: "C"
      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: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          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
  Time building chain proxies: 1.22, per 1000 atoms: 0.21
  Number of scatterers: 5869
  At special positions: 0
  Unit cell: (68.376, 74.888, 135.124, 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      34     16.00
     O    1084      8.00
     N     937      7.00
     C    3814      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 301 " - pdb=" SG  CYS A 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 460 " 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
    ALPHA1-2
      " MAN D   4 " - " MAN D   5 "
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA D   3 " - " MAN D   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
      " BMA D   3 " - " MAN D   6 "
      " MAN D   6 " - " MAN D   7 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    BETA1-6
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG A 601 " - " ASN A 146 "
      " NAG A 602 " - " ASN A 133 "
      " NAG A 603 " - " ASN A 220 "
      " NAG A 604 " - " ASN A 247 "
      " NAG A 605 " - " ASN A 241 "
      " NAG C   1 " - " ASN A 177 "
      " NAG D   1 " - " ASN A 312 "
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 315.8 milliseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 6 sheets defined
      57.4% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 68
      removed outlier: 3.624A  pdb=" N   THR A  66 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 98
    Processing helix  chain 'A' and resid 153 through 156
    Processing helix  chain 'A' and resid 192 through 196
      removed outlier: 4.225A  pdb=" N   ARG A 196 " --> pdb=" O   CYS A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
      removed outlier: 3.693A  pdb=" N   ALA A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 51
    Processing helix  chain 'B' and resid 52 through 73
      removed outlier: 4.436A  pdb=" N   TYR B  56 " --> pdb=" O   GLY B  52 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   GLN B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   ILE B  69 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 107
      Proline residue:  B  98  - end of helix
    Processing helix  chain 'B' and resid 115 through 135
      removed outlier: 3.855A  pdb=" N   ILE B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      Proline residue:  B 124  - end of helix
      removed outlier: 3.927A  pdb=" N   TRP B 134 " --> pdb=" O   TYR B 130 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 173
      removed outlier: 4.240A  pdb=" N   TRP B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   TYR B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU B 148 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
      Proline residue:  B 164  - end of helix
      removed outlier: 4.393A  pdb=" N   THR B 169 " --> pdb=" O   TYR B 165 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   MET B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   PHE B 171 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   SER B 173 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 206
    Processing helix  chain 'B' and resid 234 through 264
      removed outlier: 3.957A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 291
    Processing helix  chain 'B' and resid 292 through 322
      removed outlier: 3.917A  pdb=" N   PHE B 303 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ALA B 316 " --> pdb=" O   GLU B 312 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   LEU B 317 " --> pdb=" O   GLY B 313 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   THR B 320 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 353
      Proline residue:  B 345  - end of helix
    Processing helix  chain 'B' and resid 357 through 373
      removed outlier: 4.134A  pdb=" N   ALA B 367 " --> pdb=" O   GLY B 363 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   VAL B 368 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
      Proline residue:  B 369  - end of helix
    Processing helix  chain 'B' and resid 374 through 376
      No H-bonds generated for 'chain 'B' and resid 374 through 376'
    Processing helix  chain 'B' and resid 380 through 417
      Proline residue:  B 402  - end of helix
      removed outlier: 3.842A  pdb=" N   LEU B 406 " --> pdb=" O   PRO B 402 " (cutoff:3.500A)
      Proline residue:  B 407  - end of helix
    Processing helix  chain 'B' and resid 423 through 453
      removed outlier: 4.114A  pdb=" N   PHE B 427 " --> pdb=" O   THR B 423 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE B 428 " --> pdb=" O   GLU B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 489
      removed outlier: 3.951A  pdb=" N   LYS B 467 " --> pdb=" O   PRO B 463 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA B 477 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
      Proline residue:  B 478  - end of helix
    Processing helix  chain 'B' and resid 494 through 509
      removed outlier: 3.621A  pdb=" N   LYS B 504 " --> pdb=" O   ARG B 500 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   LEU B 509 " --> pdb=" O   ALA B 505 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 78
      removed outlier: 6.999A  pdb=" N   GLY A 268 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   HIS A 285 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   TYR A 266 " --> pdb=" O   HIS A 285 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78
      removed outlier: 3.682A  pdb=" N   THR A 290 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 136
      removed outlier: 6.453A  pdb=" N   THR A 135 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
      removed outlier: 8.531A  pdb=" N   THR A 316 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   ILE A 319 " --> pdb=" O   ILE A 125 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   ILE A 125 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   ALA A 123 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   THR A 148 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 8.573A  pdb=" N   ILE A 125 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 10.203A  pdb=" N   THR A 150 " --> pdb=" O   ILE A 125 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   VAL A 127 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
      removed outlier: 10.240A  pdb=" N   ASP A 152 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 10.085A  pdb=" N   ALA A 129 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASN A 177 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 136
      removed outlier: 6.453A  pdb=" N   THR A 135 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
      removed outlier: 8.531A  pdb=" N   THR A 316 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 160
    Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 217

    318 hydrogen bonds defined for protein.
    933 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: 1.01

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1743
        1.34 -     1.46: 1525
        1.46 -     1.58: 2713
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 6029
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.497 -0.091 2.00e-02 2.50e+03 2.07e+01
  bond pdb=" C1  MAN D   5 "
       pdb=" C2  MAN D   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.581 -0.055 2.00e-02 2.50e+03 7.49e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.66e+00
  bond pdb=" C1  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.49e+00
  bond pdb=" C2  BMA D   3 "
       pdb=" C3  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.544  1.502  0.042 2.00e-02 2.50e+03 4.35e+00
  ... (remaining 6024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 7737
        2.02 -     4.05: 378
        4.05 -     6.07: 73
        6.07 -     8.09: 20
        8.09 -    10.11: 12
  Bond angle restraints: 8220
  Sorted by residual:
  angle pdb=" C   LEU B 376 "
        pdb=" N   MET B 377 "
        pdb=" CA  MET B 377 "
      ideal   model   delta    sigma   weight residual
     121.54  130.13   -8.59 1.91e+00 2.74e-01 2.02e+01
  angle pdb=" C   ALA A 246 "
        pdb=" N   ASN A 247 "
        pdb=" CA  ASN A 247 "
      ideal   model   delta    sigma   weight residual
     121.85  129.21   -7.36 1.77e+00 3.19e-01 1.73e+01
  angle pdb=" CG  ARG B 111 "
        pdb=" CD  ARG B 111 "
        pdb=" NE  ARG B 111 "
      ideal   model   delta    sigma   weight residual
     112.00  121.12   -9.12 2.20e+00 2.07e-01 1.72e+01
  angle pdb=" N   GLY B 263 "
        pdb=" CA  GLY B 263 "
        pdb=" C   GLY B 263 "
      ideal   model   delta    sigma   weight residual
     113.18  122.79   -9.61 2.37e+00 1.78e-01 1.64e+01
  angle pdb=" CB  ARG B 353 "
        pdb=" CG  ARG B 353 "
        pdb=" CD  ARG B 353 "
      ideal   model   delta    sigma   weight residual
     111.30  119.90   -8.60 2.30e+00 1.89e-01 1.40e+01
  ... (remaining 8215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.55: 3470
       24.55 -    49.10: 223
       49.10 -    73.65: 31
       73.65 -    98.20: 22
       98.20 -   122.75: 6
  Dihedral angle restraints: 3752
    sinusoidal: 1668
      harmonic: 2084
  Sorted by residual:
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.48  -87.52     1      1.00e+01 1.00e-02 9.18e+01
  dihedral pdb=" CB  CYS A 126 "
           pdb=" SG  CYS A 126 "
           pdb=" SG  CYS A 145 "
           pdb=" CB  CYS A 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   33.80   59.20     1      1.00e+01 1.00e-02 4.68e+01
  dihedral pdb=" CA  VAL B  74 "
           pdb=" C   VAL B  74 "
           pdb=" N   ALA B  75 "
           pdb=" CA  ALA B  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 3749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 880
       0.092 -    0.183: 102
       0.183 -    0.275: 4
       0.275 -    0.366: 1
       0.366 -    0.457: 2
  Chirality restraints: 989
  Sorted by residual:
  chirality pdb=" C1  NAG A 605 "
            pdb=" ND2 ASN A 241 "
            pdb=" C2  NAG A 605 "
            pdb=" O5  NAG A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.23e+00
  chirality pdb=" C1  NAG A 603 "
            pdb=" ND2 ASN A 220 "
            pdb=" C2  NAG A 603 "
            pdb=" O5  NAG A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-01 2.50e+01 4.01e+00
  chirality pdb=" CA  ASN B 380 "
            pdb=" N   ASN B 380 "
            pdb=" C   ASN B 380 "
            pdb=" CB  ASN B 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 986 not shown)

  Planarity restraints: 1011
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 477 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO B 478 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 478 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 478 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 299 "   -0.016 2.00e-02 2.50e+03   1.52e-02 4.65e+00
        pdb=" CG  TYR A 299 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 299 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 299 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 299 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 299 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 299 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 299 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 118 "    0.017 2.00e-02 2.50e+03   1.26e-02 4.00e+00
        pdb=" CG  TRP B 118 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 118 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 118 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 118 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 118 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 118 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 118 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 118 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 118 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1008 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 167
        2.69 -     3.24: 6183
        3.24 -     3.79: 9472
        3.79 -     4.35: 11177
        4.35 -     4.90: 19019
  Nonbonded interactions: 46018
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  70 "
            pdb=" O   TRP B 134 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OH  TYR B  49 "
            pdb=" OG1 THR B 169 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER A 198 "
            pdb=" OE1 GLN A 250 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   GLN B 462 "
            pdb=" NZ  LYS B 467 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O4  NAG C   2 "
            pdb=" O5  BMA C   3 "
     model   vdw
     2.312 3.040
  ... (remaining 46013 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.820
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   12.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
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      :  0.007   0.096   6051  Z= 0.327
  Angle     :  1.105  10.113   8281  Z= 0.552
  Chirality :  0.060   0.457    989
  Planarity :  0.007   0.057   1004
  Dihedral  : 17.878 122.750   2393
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.86 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.28), residues: 710
  helix:  0.08 (0.24), residues: 368
  sheet:  0.41 (0.56), residues: 80
  loop : -2.45 (0.31), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 111 
 TYR   0.036   0.003   TYR A 299 
 PHE   0.023   0.003   PHE B 135 
 TRP   0.034   0.003   TRP B 118 
 HIS   0.012   0.002   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 ( 6029)
  covalent geometry    : angle       1.08135 ( 8220)
  SS BOND              : bond        0.00203 (    5)
  SS BOND              : angle       2.53028 (   10)
  hydrogen bonds       : bond        0.06658 (  310)
  hydrogen bonds       : angle       5.48379 (  933)
  link_ALPHA1-2        : bond        0.00930 (    1)
  link_ALPHA1-2        : angle       1.72327 (    3)
  link_ALPHA1-3        : bond        0.00139 (    2)
  link_ALPHA1-3        : angle       2.30368 (    6)
  link_ALPHA1-6        : bond        0.00288 (    3)
  link_ALPHA1-6        : angle       2.30118 (    9)
  link_BETA1-4         : bond        0.00618 (    3)
  link_BETA1-4         : angle       2.59985 (    9)
  link_BETA1-6         : bond        0.00422 (    1)
  link_BETA1-6         : angle       3.08986 (    3)
  link_NAG-ASN         : bond        0.00559 (    7)
  link_NAG-ASN         : angle       3.55695 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8983 (mttt)
REVERT: A   99 ASP cc_start: 0.8802 (t0) cc_final: 0.8573 (t0)
REVERT: A  120 MET cc_start: 0.6624 (ptm) cc_final: 0.6161 (ptp)
REVERT: A  226 GLU cc_start: 0.7435 (pt0) cc_final: 0.7086 (mt-10)
REVERT: A  227 TRP cc_start: 0.8124 (p90) cc_final: 0.7557 (p90)
REVERT: A  262 ILE cc_start: 0.8559 (tt) cc_final: 0.8323 (tt)
REVERT: A  293 LYS cc_start: 0.8707 (tttt) cc_final: 0.8488 (ttpp)
REVERT: B   69 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (mt)
REVERT: B  111 ARG cc_start: 0.4986 (ttm170) cc_final: 0.2973 (ttp-170)
REVERT: B  155 GLU cc_start: 0.8912 (tp30) cc_final: 0.8376 (mm-30)
REVERT: B  176 GLN cc_start: 0.7802 (mt0) cc_final: 0.7116 (tm-30)
REVERT: B  239 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: B  289 MET cc_start: 0.3365 (tpt) cc_final: 0.2588 (tpt)
REVERT: B  309 MET cc_start: 0.7070 (ptp) cc_final: 0.6702 (ptp)
REVERT: B  370 PHE cc_start: 0.7494 (m-80) cc_final: 0.7280 (m-10)
REVERT: B  377 MET cc_start: 0.1822 (ptt) cc_final: 0.1492 (ptt)
REVERT: B  458 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7013 (ttm-80)
  outliers start: 6
  outliers final: 1
  residues processed: 150
  average time/residue: 0.0943
  time to fit residues: 17.7537
Evaluate side-chains
  105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  317 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 105 GLN
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 GLN
B  68 GLN
B 235 HIS
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.145566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.134321 restraints weight = 12039.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.137399 restraints weight = 5843.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.139018 restraints weight = 3300.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.139737 restraints weight = 2176.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.140353 restraints weight = 1760.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6051  Z= 0.179
  Angle     :  0.789   7.769   8281  Z= 0.379
  Chirality :  0.046   0.305    989
  Planarity :  0.005   0.044   1004
  Dihedral  : 12.590 108.699   1114
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.75 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.29), residues: 710
  helix:  0.91 (0.26), residues: 366
  sheet:  0.29 (0.57), residues: 80
  loop : -2.18 (0.31), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  77 
 TYR   0.021   0.002   TYR A 299 
 PHE   0.021   0.002   PHE B 468 
 TRP   0.018   0.002   TRP B 146 
 HIS   0.005   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6029)
  covalent geometry    : angle       0.76117 ( 8220)
  SS BOND              : bond        0.00356 (    5)
  SS BOND              : angle       1.42458 (   10)
  hydrogen bonds       : bond        0.04998 (  310)
  hydrogen bonds       : angle       4.74119 (  933)
  link_ALPHA1-2        : bond        0.01144 (    1)
  link_ALPHA1-2        : angle       1.35670 (    3)
  link_ALPHA1-3        : bond        0.00788 (    2)
  link_ALPHA1-3        : angle       1.47850 (    6)
  link_ALPHA1-6        : bond        0.00567 (    3)
  link_ALPHA1-6        : angle       2.62721 (    9)
  link_BETA1-4         : bond        0.00498 (    3)
  link_BETA1-4         : angle       2.98479 (    9)
  link_BETA1-6         : bond        0.00572 (    1)
  link_BETA1-6         : angle       4.34655 (    3)
  link_NAG-ASN         : bond        0.00375 (    7)
  link_NAG-ASN         : angle       2.73480 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8784 (t0) cc_final: 0.8582 (t0)
REVERT: A  114 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6974 (m-80)
REVERT: A  120 MET cc_start: 0.7202 (ptm) cc_final: 0.6943 (ptp)
REVERT: A  262 ILE cc_start: 0.9086 (tt) cc_final: 0.8814 (tt)
REVERT: B  111 ARG cc_start: 0.5415 (ttm170) cc_final: 0.2896 (ttm170)
REVERT: B  239 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: B  289 MET cc_start: 0.3101 (tpt) cc_final: 0.2215 (tpt)
  outliers start: 23
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0833
  time to fit residues: 14.1852
Evaluate side-chains
  115 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0980
   chunk 40 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 59 optimal weight:    7.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
B 419 HIS
** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.140727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.128592 restraints weight = 11837.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.131110 restraints weight = 6191.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.132822 restraints weight = 3852.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133950 restraints weight = 2655.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.134679 restraints weight = 2001.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   6051  Z= 0.251
  Angle     :  0.843   8.251   8281  Z= 0.405
  Chirality :  0.050   0.385    989
  Planarity :  0.006   0.079   1004
  Dihedral  : 11.111 101.193   1110
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 20.93 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.30), residues: 710
  helix:  0.81 (0.26), residues: 365
  sheet:  0.21 (0.59), residues: 80
  loop : -2.29 (0.32), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 111 
 TYR   0.020   0.002   TYR A 299 
 PHE   0.022   0.002   PHE B 350 
 TRP   0.027   0.002   TRP B 118 
 HIS   0.005   0.001   HIS B 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 ( 6029)
  covalent geometry    : angle       0.81403 ( 8220)
  SS BOND              : bond        0.00245 (    5)
  SS BOND              : angle       1.86560 (   10)
  hydrogen bonds       : bond        0.05093 (  310)
  hydrogen bonds       : angle       4.79501 (  933)
  link_ALPHA1-2        : bond        0.01297 (    1)
  link_ALPHA1-2        : angle       1.31585 (    3)
  link_ALPHA1-3        : bond        0.00884 (    2)
  link_ALPHA1-3        : angle       1.54686 (    6)
  link_ALPHA1-6        : bond        0.00506 (    3)
  link_ALPHA1-6        : angle       2.82857 (    9)
  link_BETA1-4         : bond        0.00441 (    3)
  link_BETA1-4         : angle       2.95599 (    9)
  link_BETA1-6         : bond        0.00352 (    1)
  link_BETA1-6         : angle       3.95991 (    3)
  link_NAG-ASN         : bond        0.00539 (    7)
  link_NAG-ASN         : angle       2.96603 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 107
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8842 (t0) cc_final: 0.8608 (t0)
REVERT: A  114 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7115 (m-80)
REVERT: B  111 ARG cc_start: 0.5611 (ttm170) cc_final: 0.3585 (ttm110)
REVERT: B  239 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: B  289 MET cc_start: 0.3183 (tpt) cc_final: 0.2232 (tpt)
REVERT: B  378 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.1323 (mt-10)
REVERT: B  414 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7358 (t-90)
REVERT: B  431 TYR cc_start: 0.8084 (t80) cc_final: 0.7862 (t80)
  outliers start: 32
  outliers final: 24
  residues processed: 129
  average time/residue: 0.0813
  time to fit residues: 13.7466
Evaluate side-chains
  132 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  378 GLU
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 58 optimal weight:    0.0980
   chunk 50 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0010
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
B 421 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.145395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.133559 restraints weight = 11915.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.136230 restraints weight = 6025.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.137972 restraints weight = 3638.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.139001 restraints weight = 2486.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.139868 restraints weight = 1891.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6051  Z= 0.139
  Angle     :  0.712   6.744   8281  Z= 0.339
  Chirality :  0.043   0.256    989
  Planarity :  0.005   0.066   1004
  Dihedral  :  9.648  96.846   1110
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 23.03 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.30), residues: 710
  helix:  1.00 (0.26), residues: 365
  sheet:  0.10 (0.59), residues: 80
  loop : -2.20 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  63 
 TYR   0.016   0.001   TYR A 299 
 PHE   0.019   0.001   PHE B 468 
 TRP   0.025   0.002   TRP B 118 
 HIS   0.005   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6029)
  covalent geometry    : angle       0.68921 ( 8220)
  SS BOND              : bond        0.00679 (    5)
  SS BOND              : angle       1.18276 (   10)
  hydrogen bonds       : bond        0.04600 (  310)
  hydrogen bonds       : angle       4.49889 (  933)
  link_ALPHA1-2        : bond        0.00978 (    1)
  link_ALPHA1-2        : angle       1.27622 (    3)
  link_ALPHA1-3        : bond        0.01027 (    2)
  link_ALPHA1-3        : angle       1.26992 (    6)
  link_ALPHA1-6        : bond        0.00735 (    3)
  link_ALPHA1-6        : angle       2.46850 (    9)
  link_BETA1-4         : bond        0.00507 (    3)
  link_BETA1-4         : angle       2.51784 (    9)
  link_BETA1-6         : bond        0.00458 (    1)
  link_BETA1-6         : angle       2.79127 (    3)
  link_NAG-ASN         : bond        0.00308 (    7)
  link_NAG-ASN         : angle       2.46281 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8801 (t0) cc_final: 0.8561 (t0)
REVERT: A  114 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6874 (m-80)
REVERT: B  111 ARG cc_start: 0.5484 (ttm170) cc_final: 0.2425 (ttp-170)
REVERT: B  239 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: B  289 MET cc_start: 0.2928 (tpt) cc_final: 0.2037 (tpt)
REVERT: B  309 MET cc_start: 0.7617 (ptp) cc_final: 0.7204 (ptp)
REVERT: B  370 PHE cc_start: 0.6728 (m-10) cc_final: 0.6502 (m-10)
REVERT: B  377 MET cc_start: 0.2775 (OUTLIER) cc_final: 0.1951 (ttp)
REVERT: B  431 TYR cc_start: 0.8031 (t80) cc_final: 0.7793 (t80)
  outliers start: 30
  outliers final: 19
  residues processed: 136
  average time/residue: 0.0789
  time to fit residues: 14.0208
Evaluate side-chains
  127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0070
   chunk 10 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 51 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.145421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.133772 restraints weight = 12165.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.136405 restraints weight = 6216.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.138113 restraints weight = 3775.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.139231 restraints weight = 2585.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140009 restraints weight = 1939.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6051  Z= 0.136
  Angle     :  0.732  12.836   8281  Z= 0.340
  Chirality :  0.044   0.317    989
  Planarity :  0.005   0.057   1004
  Dihedral  :  8.878  89.284   1110
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 25.12 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.30), residues: 710
  helix:  1.04 (0.26), residues: 365
  sheet:  0.14 (0.58), residues: 80
  loop : -2.15 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  63 
 TYR   0.014   0.001   TYR A 266 
 PHE   0.015   0.001   PHE B 468 
 TRP   0.023   0.002   TRP B 118 
 HIS   0.006   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6029)
  covalent geometry    : angle       0.70218 ( 8220)
  SS BOND              : bond        0.00182 (    5)
  SS BOND              : angle       1.84141 (   10)
  hydrogen bonds       : bond        0.04405 (  310)
  hydrogen bonds       : angle       4.43051 (  933)
  link_ALPHA1-2        : bond        0.00899 (    1)
  link_ALPHA1-2        : angle       1.30743 (    3)
  link_ALPHA1-3        : bond        0.01015 (    2)
  link_ALPHA1-3        : angle       1.30417 (    6)
  link_ALPHA1-6        : bond        0.00758 (    3)
  link_ALPHA1-6        : angle       2.61150 (    9)
  link_BETA1-4         : bond        0.00473 (    3)
  link_BETA1-4         : angle       2.38753 (    9)
  link_BETA1-6         : bond        0.00420 (    1)
  link_BETA1-6         : angle       2.68778 (    3)
  link_NAG-ASN         : bond        0.00281 (    7)
  link_NAG-ASN         : angle       3.04989 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8749 (t0) cc_final: 0.8523 (t0)
REVERT: A  114 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6812 (m-80)
REVERT: B  111 ARG cc_start: 0.5552 (ttm170) cc_final: 0.1902 (ttp-110)
REVERT: B  239 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: B  289 MET cc_start: 0.3035 (tpt) cc_final: 0.2081 (tpt)
REVERT: B  309 MET cc_start: 0.7521 (ptp) cc_final: 0.7189 (ptp)
REVERT: B  370 PHE cc_start: 0.6615 (m-10) cc_final: 0.6389 (m-10)
REVERT: B  377 MET cc_start: 0.2816 (OUTLIER) cc_final: 0.1945 (ttp)
REVERT: B  431 TYR cc_start: 0.8026 (t80) cc_final: 0.7762 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 130
  average time/residue: 0.0830
  time to fit residues: 14.0680
Evaluate side-chains
  128 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.142607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.130814 restraints weight = 11949.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.133358 restraints weight = 6239.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135044 restraints weight = 3847.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.136168 restraints weight = 2659.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.136839 restraints weight = 2004.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6051  Z= 0.196
  Angle     :  0.761   7.736   8281  Z= 0.362
  Chirality :  0.045   0.328    989
  Planarity :  0.005   0.058   1004
  Dihedral  :  8.408  71.343   1110
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 24.80 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.30), residues: 710
  helix:  1.01 (0.26), residues: 365
  sheet:  0.01 (0.58), residues: 80
  loop : -2.26 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  77 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.014   0.001   PHE B 468 
 TRP   0.022   0.002   TRP B 118 
 HIS   0.004   0.001   HIS B 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6029)
  covalent geometry    : angle       0.73353 ( 8220)
  SS BOND              : bond        0.00272 (    5)
  SS BOND              : angle       1.92089 (   10)
  hydrogen bonds       : bond        0.04508 (  310)
  hydrogen bonds       : angle       4.52079 (  933)
  link_ALPHA1-2        : bond        0.01020 (    1)
  link_ALPHA1-2        : angle       1.32252 (    3)
  link_ALPHA1-3        : bond        0.01007 (    2)
  link_ALPHA1-3        : angle       1.42909 (    6)
  link_ALPHA1-6        : bond        0.00701 (    3)
  link_ALPHA1-6        : angle       3.01671 (    9)
  link_BETA1-4         : bond        0.00404 (    3)
  link_BETA1-4         : angle       2.53340 (    9)
  link_BETA1-6         : bond        0.00196 (    1)
  link_BETA1-6         : angle       2.97852 (    3)
  link_NAG-ASN         : bond        0.00357 (    7)
  link_NAG-ASN         : angle       2.70590 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 107
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8793 (t0) cc_final: 0.8550 (t0)
REVERT: A  114 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6938 (m-80)
REVERT: B  111 ARG cc_start: 0.5559 (ttm170) cc_final: 0.3771 (ttm170)
REVERT: B  239 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8160 (tm-30)
REVERT: B  285 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4328 (tt)
REVERT: B  289 MET cc_start: 0.3145 (tpt) cc_final: 0.2181 (tpt)
REVERT: B  309 MET cc_start: 0.7600 (ptp) cc_final: 0.7340 (ptp)
REVERT: B  370 PHE cc_start: 0.6651 (m-10) cc_final: 0.6427 (m-10)
REVERT: B  377 MET cc_start: 0.3020 (OUTLIER) cc_final: 0.2141 (ttp)
REVERT: B  431 TYR cc_start: 0.8052 (t80) cc_final: 0.7822 (t80)
  outliers start: 36
  outliers final: 26
  residues processed: 133
  average time/residue: 0.0776
  time to fit residues: 13.5355
Evaluate side-chains
  130 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  414 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  497 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0970
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0070
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.145170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.133673 restraints weight = 12018.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.136238 restraints weight = 6210.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.137903 restraints weight = 3797.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.139055 restraints weight = 2611.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.139740 restraints weight = 1957.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6051  Z= 0.136
  Angle     :  0.722  11.087   8281  Z= 0.338
  Chirality :  0.042   0.252    989
  Planarity :  0.004   0.052   1004
  Dihedral  :  7.416  54.031   1110
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 25.93 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.30), residues: 710
  helix:  1.09 (0.26), residues: 364
  sheet:  0.03 (0.58), residues: 80
  loop : -2.19 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  77 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.010   0.001   PHE B 468 
 TRP   0.021   0.002   TRP B 118 
 HIS   0.006   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6029)
  covalent geometry    : angle       0.69956 ( 8220)
  SS BOND              : bond        0.00393 (    5)
  SS BOND              : angle       1.78142 (   10)
  hydrogen bonds       : bond        0.04330 (  310)
  hydrogen bonds       : angle       4.39484 (  933)
  link_ALPHA1-2        : bond        0.00874 (    1)
  link_ALPHA1-2        : angle       1.32241 (    3)
  link_ALPHA1-3        : bond        0.00995 (    2)
  link_ALPHA1-3        : angle       1.19955 (    6)
  link_ALPHA1-6        : bond        0.00910 (    3)
  link_ALPHA1-6        : angle       2.52688 (    9)
  link_BETA1-4         : bond        0.00444 (    3)
  link_BETA1-4         : angle       2.26553 (    9)
  link_BETA1-6         : bond        0.00339 (    1)
  link_BETA1-6         : angle       2.49382 (    3)
  link_NAG-ASN         : bond        0.00302 (    7)
  link_NAG-ASN         : angle       2.49858 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8760 (t0) cc_final: 0.8503 (t0)
REVERT: A  114 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6834 (m-80)
REVERT: B  111 ARG cc_start: 0.5506 (ttm170) cc_final: 0.2502 (ttp-170)
REVERT: B  132 LEU cc_start: 0.9030 (tp) cc_final: 0.8766 (tp)
REVERT: B  239 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8114 (tm-30)
REVERT: B  285 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4268 (tt)
REVERT: B  289 MET cc_start: 0.3019 (tpt) cc_final: 0.2070 (tpt)
REVERT: B  370 PHE cc_start: 0.6568 (m-10) cc_final: 0.6286 (m-10)
REVERT: B  377 MET cc_start: 0.2942 (OUTLIER) cc_final: 0.2050 (ttp)
REVERT: B  431 TYR cc_start: 0.8033 (t80) cc_final: 0.7753 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 134
  average time/residue: 0.0725
  time to fit residues: 12.8664
Evaluate side-chains
  133 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  497 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 52 optimal weight:    0.0470
   chunk 44 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.145486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133980 restraints weight = 12064.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.136533 restraints weight = 6238.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.138177 restraints weight = 3825.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.139318 restraints weight = 2631.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.140091 restraints weight = 1973.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6051  Z= 0.140
  Angle     :  0.760  12.316   8281  Z= 0.354
  Chirality :  0.045   0.378    989
  Planarity :  0.005   0.052   1004
  Dihedral  :  6.772  43.412   1110
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 26.57 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.30), residues: 710
  helix:  1.07 (0.26), residues: 365
  sheet:  0.11 (0.59), residues: 80
  loop : -2.17 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  77 
 TYR   0.013   0.001   TYR A 299 
 PHE   0.010   0.001   PHE B 154 
 TRP   0.020   0.002   TRP B 118 
 HIS   0.004   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6029)
  covalent geometry    : angle       0.72089 ( 8220)
  SS BOND              : bond        0.00265 (    5)
  SS BOND              : angle       2.57927 (   10)
  hydrogen bonds       : bond        0.04269 (  310)
  hydrogen bonds       : angle       4.41146 (  933)
  link_ALPHA1-2        : bond        0.00834 (    1)
  link_ALPHA1-2        : angle       1.33857 (    3)
  link_ALPHA1-3        : bond        0.00985 (    2)
  link_ALPHA1-3        : angle       1.26755 (    6)
  link_ALPHA1-6        : bond        0.01011 (    3)
  link_ALPHA1-6        : angle       2.59877 (    9)
  link_BETA1-4         : bond        0.00410 (    3)
  link_BETA1-4         : angle       2.24186 (    9)
  link_BETA1-6         : bond        0.00358 (    1)
  link_BETA1-6         : angle       2.46483 (    3)
  link_NAG-ASN         : bond        0.00258 (    7)
  link_NAG-ASN         : angle       3.79358 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8738 (t0) cc_final: 0.8484 (t0)
REVERT: A  114 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6814 (m-80)
REVERT: B  111 ARG cc_start: 0.5481 (ttm170) cc_final: 0.2071 (ttp-170)
REVERT: B  132 LEU cc_start: 0.9023 (tp) cc_final: 0.8755 (tp)
REVERT: B  239 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: B  285 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4274 (tt)
REVERT: B  289 MET cc_start: 0.2958 (tpt) cc_final: 0.2035 (tpt)
REVERT: B  309 MET cc_start: 0.7366 (ptp) cc_final: 0.7088 (ptp)
REVERT: B  370 PHE cc_start: 0.6544 (m-80) cc_final: 0.6250 (m-10)
REVERT: B  377 MET cc_start: 0.2936 (OUTLIER) cc_final: 0.2027 (ttp)
REVERT: B  415 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8951 (pp)
REVERT: B  431 TYR cc_start: 0.8018 (t80) cc_final: 0.7749 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 129
  average time/residue: 0.0793
  time to fit residues: 13.3577
Evaluate side-chains
  135 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 58 optimal weight:    0.2980
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
B 214 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.145265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.133528 restraints weight = 12184.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.136150 restraints weight = 6267.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.137860 restraints weight = 3807.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.139008 restraints weight = 2610.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.139789 restraints weight = 1946.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6051  Z= 0.151
  Angle     :  0.747  10.106   8281  Z= 0.351
  Chirality :  0.044   0.347    989
  Planarity :  0.005   0.051   1004
  Dihedral  :  6.557  42.473   1110
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 25.60 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.30), residues: 710
  helix:  1.08 (0.26), residues: 365
  sheet:  0.12 (0.59), residues: 80
  loop : -2.17 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  77 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.011   0.001   PHE B 154 
 TRP   0.019   0.001   TRP B 118 
 HIS   0.003   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6029)
  covalent geometry    : angle       0.71416 ( 8220)
  SS BOND              : bond        0.00259 (    5)
  SS BOND              : angle       2.17885 (   10)
  hydrogen bonds       : bond        0.04226 (  310)
  hydrogen bonds       : angle       4.39850 (  933)
  link_ALPHA1-2        : bond        0.00845 (    1)
  link_ALPHA1-2        : angle       1.33590 (    3)
  link_ALPHA1-3        : bond        0.00950 (    2)
  link_ALPHA1-3        : angle       1.30109 (    6)
  link_ALPHA1-6        : bond        0.00966 (    3)
  link_ALPHA1-6        : angle       2.63963 (    9)
  link_BETA1-4         : bond        0.00390 (    3)
  link_BETA1-4         : angle       2.28168 (    9)
  link_BETA1-6         : bond        0.00289 (    1)
  link_BETA1-6         : angle       2.51512 (    3)
  link_NAG-ASN         : bond        0.00311 (    7)
  link_NAG-ASN         : angle       3.32299 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8775 (t0) cc_final: 0.8497 (t0)
REVERT: A  114 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6985 (m-80)
REVERT: B  111 ARG cc_start: 0.5468 (ttm170) cc_final: 0.2337 (ttp-170)
REVERT: B  239 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: B  285 LEU cc_start: 0.5004 (OUTLIER) cc_final: 0.4278 (tt)
REVERT: B  289 MET cc_start: 0.3010 (tpt) cc_final: 0.2081 (tpt)
REVERT: B  309 MET cc_start: 0.7491 (ptp) cc_final: 0.7218 (ptp)
REVERT: B  370 PHE cc_start: 0.6620 (m-80) cc_final: 0.6292 (m-10)
REVERT: B  377 MET cc_start: 0.2940 (OUTLIER) cc_final: 0.2022 (ttp)
REVERT: B  415 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8892 (pp)
REVERT: B  431 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7782 (t80)
  outliers start: 32
  outliers final: 24
  residues processed: 135
  average time/residue: 0.0744
  time to fit residues: 13.2822
Evaluate side-chains
  139 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  431 TYR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  497 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0060
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 GLN
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.145504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133925 restraints weight = 12187.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.136463 restraints weight = 6341.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.138149 restraints weight = 3890.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.139271 restraints weight = 2673.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.140047 restraints weight = 1994.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6051  Z= 0.145
  Angle     :  0.745   9.499   8281  Z= 0.351
  Chirality :  0.044   0.317    989
  Planarity :  0.005   0.052   1004
  Dihedral  :  6.411  42.015   1110
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 26.41 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.30), residues: 710
  helix:  1.06 (0.26), residues: 365
  sheet:  0.14 (0.59), residues: 80
  loop : -2.15 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  77 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.011   0.001   PHE B 154 
 TRP   0.020   0.002   TRP B 118 
 HIS   0.003   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6029)
  covalent geometry    : angle       0.71625 ( 8220)
  SS BOND              : bond        0.00269 (    5)
  SS BOND              : angle       2.01347 (   10)
  hydrogen bonds       : bond        0.04209 (  310)
  hydrogen bonds       : angle       4.37054 (  933)
  link_ALPHA1-2        : bond        0.00840 (    1)
  link_ALPHA1-2        : angle       1.34261 (    3)
  link_ALPHA1-3        : bond        0.00947 (    2)
  link_ALPHA1-3        : angle       1.28054 (    6)
  link_ALPHA1-6        : bond        0.00928 (    3)
  link_ALPHA1-6        : angle       2.48163 (    9)
  link_BETA1-4         : bond        0.00392 (    3)
  link_BETA1-4         : angle       2.24866 (    9)
  link_BETA1-6         : bond        0.00312 (    1)
  link_BETA1-6         : angle       2.46714 (    3)
  link_NAG-ASN         : bond        0.00321 (    7)
  link_NAG-ASN         : angle       3.16519 (   21)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.8666 (t0) cc_final: 0.8457 (t0)
REVERT: A  114 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6947 (m-80)
REVERT: B  111 ARG cc_start: 0.5522 (ttm170) cc_final: 0.2386 (ttp-170)
REVERT: B  237 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6779 (pt0)
REVERT: B  239 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8151 (tm-30)
REVERT: B  285 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4283 (tt)
REVERT: B  289 MET cc_start: 0.2977 (tpt) cc_final: 0.2049 (tpt)
REVERT: B  309 MET cc_start: 0.7470 (ptp) cc_final: 0.7223 (ptp)
REVERT: B  370 PHE cc_start: 0.6578 (m-80) cc_final: 0.6268 (m-10)
REVERT: B  377 MET cc_start: 0.2971 (OUTLIER) cc_final: 0.2048 (ttp)
REVERT: B  415 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8883 (pp)
REVERT: B  431 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7755 (t80)
  outliers start: 29
  outliers final: 24
  residues processed: 130
  average time/residue: 0.0761
  time to fit residues: 13.0986
Evaluate side-chains
  138 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  114 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  431 TYR
Chi-restraints excluded: chain B residue  452 PHE
Chi-restraints excluded: chain B residue  472 MET
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  497 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 42 optimal weight:    0.3980
   chunk 58 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN
** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.145315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.133515 restraints weight = 11925.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.136141 restraints weight = 6097.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.137887 restraints weight = 3681.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.139056 restraints weight = 2497.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.139792 restraints weight = 1840.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6051  Z= 0.154
  Angle     :  0.743   9.032   8281  Z= 0.351
  Chirality :  0.044   0.319    989
  Planarity :  0.005   0.052   1004
  Dihedral  :  6.362  42.211   1110
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 25.93 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.30), residues: 710
  helix:  1.09 (0.26), residues: 365
  sheet:  0.14 (0.59), residues: 80
  loop : -2.18 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  77 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.011   0.001   PHE B 154 
 TRP   0.020   0.002   TRP B 118 
 HIS   0.003   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6029)
  covalent geometry    : angle       0.71402 ( 8220)
  SS BOND              : bond        0.00266 (    5)
  SS BOND              : angle       1.97143 (   10)
  hydrogen bonds       : bond        0.04207 (  310)
  hydrogen bonds       : angle       4.37163 (  933)
  link_ALPHA1-2        : bond        0.00841 (    1)
  link_ALPHA1-2        : angle       1.33398 (    3)
  link_ALPHA1-3        : bond        0.00923 (    2)
  link_ALPHA1-3        : angle       1.30712 (    6)
  link_ALPHA1-6        : bond        0.00876 (    3)
  link_ALPHA1-6        : angle       2.50128 (    9)
  link_BETA1-4         : bond        0.00379 (    3)
  link_BETA1-4         : angle       2.28102 (    9)
  link_BETA1-6         : bond        0.00281 (    1)
  link_BETA1-6         : angle       2.50955 (    3)
  link_NAG-ASN         : bond        0.00324 (    7)
  link_NAG-ASN         : angle       3.08529 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1200.51 seconds
wall clock time: 21 minutes 22.97 seconds (1282.97 seconds total)