Starting phenix.real_space_refine
on Thu Jul 24 19:25:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xo9_33341/07_2025/7xo9_33341.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xo9_33341/07_2025/7xo9_33341.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xo9_33341/07_2025/7xo9_33341.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xo9_33341/07_2025/7xo9_33341.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xo9_33341/07_2025/7xo9_33341.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xo9_33341/07_2025/7xo9_33341.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     Cl      1      4.86       5
     C    4154      2.51       5
     N    1074      2.21       5
     O    1216      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6483
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1582
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
    Chain: "D"
      Number of atoms: 4857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "D"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 44
          Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 6.13, per 1000 atoms: 0.95
  Number of scatterers: 6483
  At special positions: 0
  Unit cell: (97.232, 70.864, 117.832, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Cl      1     17.00
     S      37     16.00
     O    1216      8.00
     N    1074      7.00
     C    4154      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG D 903 " - " ASN D 546 "
      " NAG D 904 " - " ASN D 322 "
      " NAG D 905 " - " ASN D  90 "
  Time building additional restraints: 1.59
  Conformation dependent library (CDL) restraints added in 893.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 902 "
        pdb="ZN    ZN D 902 " - pdb=" NE2 HIS D 374 "


  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      55.4% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 3.606A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.356A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
      removed outlier: 3.776A  pdb=" N   ASP A 420 " --> pdb=" O   GLY A 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.653A  pdb=" N   GLN D  24 " --> pdb=" O   THR D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.617A  pdb=" N   GLN D 102 " --> pdb=" O   GLN D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 4.002A  pdb=" N   SER D 106 " --> pdb=" O   ASN D 103 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL D 107 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU D 108 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 103 through 108'
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 194
      removed outlier: 3.616A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   LYS D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLN D 175 " --> pdb=" O   GLU D 171 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
      removed outlier: 3.649A  pdb=" N   GLU D 182 " --> pdb=" O   PRO D 178 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 218 through 252
      removed outlier: 3.956A  pdb=" N   LEU D 222 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU D 232 " --> pdb=" O   HIS D 228 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
      removed outlier: 4.750A  pdb=" N   ASN D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ALA D 251 " --> pdb=" O   LYS D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 279
    Processing helix  chain 'D' and resid 293 through 299
    Processing helix  chain 'D' and resid 303 through 319
      removed outlier: 3.504A  pdb=" N   GLY D 319 " --> pdb=" O   PHE D 315 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 331
      removed outlier: 3.867A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.671A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 413
      removed outlier: 3.919A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 444
    Processing helix  chain 'D' and resid 449 through 466
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 485
    Processing helix  chain 'D' and resid 499 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 531
      removed outlier: 3.542A  pdb=" N   THR D 519 " --> pdb=" O   TYR D 515 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLN D 531 " --> pdb=" O   GLU D 527 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.743A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 574
      removed outlier: 3.597A  pdb=" N   VAL D 573 " --> pdb=" O   ALA D 569 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 581 through 588
    Processing helix  chain 'D' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356
      removed outlier: 3.540A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.602A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 132
      removed outlier: 3.645A  pdb=" N   VAL D 132 " --> pdb=" O   LEU D 142 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU D 142 " --> pdb=" O   VAL D 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.073A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352
      removed outlier: 6.027A  pdb=" N   ASP D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.77 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: 2040
        1.34 -     1.45: 1106
        1.45 -     1.57: 3462
        1.57 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 6666
  Sorted by residual:
  bond pdb=" N   ASN D 322 "
       pdb=" CA  ASN D 322 "
    ideal  model  delta    sigma   weight residual
    1.453  1.481 -0.028 1.31e-02 5.83e+03 4.65e+00
  bond pdb=" N   SER D  19 "
       pdb=" CA  SER D  19 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   ASN A 331 "
       pdb=" CA  ASN A 331 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" C3  NAG D 904 "
       pdb=" O3  NAG D 904 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.07e+00
  bond pdb=" C3  NAG D 905 "
       pdb=" O3  NAG D 905 "
    ideal  model  delta    sigma   weight residual
    1.403  1.429 -0.026 2.00e-02 2.50e+03 1.68e+00
  ... (remaining 6661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 8884
        1.33 -     2.65: 112
        2.65 -     3.98: 53
        3.98 -     5.31: 9
        5.31 -     6.63: 2
  Bond angle restraints: 9060
  Sorted by residual:
  angle pdb=" C   ASN D 322 "
        pdb=" CA  ASN D 322 "
        pdb=" CB  ASN D 322 "
      ideal   model   delta    sigma   weight residual
     109.76  116.39   -6.63 1.99e+00 2.53e-01 1.11e+01
  angle pdb=" C   ASN D 322 "
        pdb=" N   MET D 323 "
        pdb=" CA  MET D 323 "
      ideal   model   delta    sigma   weight residual
     120.87  126.40   -5.53 1.69e+00 3.50e-01 1.07e+01
  angle pdb=" CA  ASN D 322 "
        pdb=" C   ASN D 322 "
        pdb=" O   ASN D 322 "
      ideal   model   delta    sigma   weight residual
     121.81  118.90    2.91 1.18e+00 7.18e-01 6.09e+00
  angle pdb=" N   ILE D 544 "
        pdb=" CA  ILE D 544 "
        pdb=" C   ILE D 544 "
      ideal   model   delta    sigma   weight residual
     112.98  110.04    2.94 1.25e+00 6.40e-01 5.53e+00
  angle pdb=" O   PRO D 321 "
        pdb=" C   PRO D 321 "
        pdb=" N   ASN D 322 "
      ideal   model   delta    sigma   weight residual
     123.06  120.18    2.88 1.23e+00 6.61e-01 5.48e+00
  ... (remaining 9055 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 3643
       17.84 -    35.69: 249
       35.69 -    53.53: 43
       53.53 -    71.37: 13
       71.37 -    89.22: 6
  Dihedral angle restraints: 3954
    sinusoidal: 1626
      harmonic: 2328
  Sorted by residual:
  dihedral pdb=" CA  LYS D  68 "
           pdb=" CB  LYS D  68 "
           pdb=" CG  LYS D  68 "
           pdb=" CD  LYS D  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.09   59.91     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LYS D 341 "
           pdb=" CA  LYS D 341 "
           pdb=" CB  LYS D 341 "
           pdb=" CG  LYS D 341 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.74  -58.26     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CB  MET D 323 "
           pdb=" CG  MET D 323 "
           pdb=" SD  MET D 323 "
           pdb=" CE  MET D 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.17   57.83     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 3951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.249: 952
       0.249 -    0.498: 0
       0.498 -    0.747: 0
       0.747 -    0.995: 0
       0.995 -    1.244: 1
  Chirality restraints: 953
  Sorted by residual:
  chirality pdb=" C1  NAG D 905 "
            pdb=" ND2 ASN D  90 "
            pdb=" C2  NAG D 905 "
            pdb=" O5  NAG D 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.16   -1.24 2.00e-01 2.50e+01 3.87e+01
  chirality pdb=" C1  NAG D 903 "
            pdb=" ND2 ASN D 546 "
            pdb=" C2  NAG D 903 "
            pdb=" O5  NAG D 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  ASN D 322 "
            pdb=" N   ASN D 322 "
            pdb=" C   ASN D 322 "
            pdb=" CB  ASN D 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.18e-01
  ... (remaining 950 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D 905 "    0.245 2.00e-02 2.50e+03   2.10e-01 5.50e+02
        pdb=" C7  NAG D 905 "   -0.054 2.00e-02 2.50e+03
        pdb=" C8  NAG D 905 "   -0.028 2.00e-02 2.50e+03
        pdb=" N2  NAG D 905 "   -0.349 2.00e-02 2.50e+03
        pdb=" O7  NAG D 905 "    0.186 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D 903 "   -0.247 2.00e-02 2.50e+03   2.08e-01 5.43e+02
        pdb=" C7  NAG D 903 "    0.063 2.00e-02 2.50e+03
        pdb=" C8  NAG D 903 "   -0.166 2.00e-02 2.50e+03
        pdb=" N2  NAG D 903 "    0.353 2.00e-02 2.50e+03
        pdb=" O7  NAG D 903 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D 904 "    0.054 2.00e-02 2.50e+03   4.46e-02 2.48e+01
        pdb=" C7  NAG D 904 "   -0.016 2.00e-02 2.50e+03
        pdb=" C8  NAG D 904 "    0.042 2.00e-02 2.50e+03
        pdb=" N2  NAG D 904 "   -0.070 2.00e-02 2.50e+03
        pdb=" O7  NAG D 904 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 75
        2.63 -     3.20: 6069
        3.20 -     3.76: 10152
        3.76 -     4.33: 14209
        4.33 -     4.90: 23577
  Nonbonded interactions: 54082
  Sorted by model distance:
  nonbonded pdb=" O   ALA D 501 "
            pdb=" OG  SER D 507 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" O   GLN D 388 "
            pdb=" NH1 ARG D 393 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" OE2 GLU D 402 "
            pdb="ZN    ZN D 902 "
     model   vdw
     2.186 2.230
  nonbonded pdb=" O   TYR D 515 "
            pdb=" OG1 THR D 519 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OG  SER D 331 "
            pdb=" O   ILE D 358 "
     model   vdw
     2.250 3.040
  ... (remaining 54077 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.170
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:13.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
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      :  0.003   0.155   6671  Z= 0.135
  Angle     :  0.561  19.811   9071  Z= 0.272
  Chirality :  0.056   1.244    953
  Planarity :  0.009   0.210   1172
  Dihedral  : 13.058  89.215   2457
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.27), residues: 789
  helix: -0.48 (0.24), residues: 396
  sheet: -1.57 (0.71), residues: 45
  loop : -1.92 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP D 165 
 HIS   0.001   0.000   HIS D 535 
 PHE   0.005   0.001   PHE A 515 
 TYR   0.007   0.001   TYR A 369 
 ARG   0.002   0.000   ARG D 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02086 (    3)
  link_NAG-ASN         : angle       9.60581 (    9)
  hydrogen bonds       : bond        0.16039 (  300)
  hydrogen bonds       : angle       5.48091 (  846)
  metal coordination   : bond        0.15493 (    1)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.25074 (    2)
  covalent geometry    : bond        0.00226 ( 6666)
  covalent geometry    : angle       0.47213 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8069 (p0) cc_final: 0.7819 (p0)
REVERT: D   37 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6286 (mt-10)
REVERT: D   94 LYS cc_start: 0.7854 (tttt) cc_final: 0.7561 (ttpp)
REVERT: D  270 MET cc_start: 0.7896 (tpp) cc_final: 0.7637 (tpt)
REVERT: D  294 THR cc_start: 0.6608 (p) cc_final: 0.6075 (p)
REVERT: D  295 ASP cc_start: 0.6696 (p0) cc_final: 0.6268 (t0)
REVERT: D  556 ASN cc_start: 0.7117 (m-40) cc_final: 0.6900 (m-40)
REVERT: D  589 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6439 (tp30)
REVERT: D  613 TYR cc_start: 0.6279 (p90) cc_final: 0.5932 (p90)
  outliers start: 0
  outliers final: 2
  residues processed: 200
  average time/residue: 1.1773
  time to fit residues: 247.2881
Evaluate side-chains
  150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain D residue  597 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0070
   chunk 61 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0060
   chunk 70 optimal weight:    0.0970
   overall best weight:    0.1212

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
A 437 ASN
A 439 ASN
A 448 ASN
A 460 ASN
A 474 GLN
A 481 ASN
D  51 ASN
D  96 GLN
D 101 GLN
D 149 ASN
D 300 GLN
D 373 HIS
D 401 HIS
D 505 HIS
D 522 GLN
D 524 GLN
D 578 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.142990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.128273 restraints weight = 9180.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 1.91
r_work: 0.3602 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6671  Z= 0.123
  Angle     :  0.555   9.952   9071  Z= 0.280
  Chirality :  0.041   0.132    953
  Planarity :  0.004   0.037   1172
  Dihedral  :  3.634  29.008    929
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 19.25 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.29), residues: 789
  helix:  0.43 (0.26), residues: 403
  sheet: -0.84 (0.78), residues: 45
  loop : -1.16 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 203 
 HIS   0.005   0.001   HIS D 374 
 PHE   0.021   0.002   PHE D 555 
 TYR   0.018   0.001   TYR A 369 
 ARG   0.006   0.001   ARG D 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00238 (    3)
  link_NAG-ASN         : angle       3.41196 (    9)
  hydrogen bonds       : bond        0.04224 (  300)
  hydrogen bonds       : angle       4.57197 (  846)
  metal coordination   : bond        0.00605 (    1)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.34122 (    2)
  covalent geometry    : bond        0.00272 ( 6666)
  covalent geometry    : angle       0.54436 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.3695 (OUTLIER) cc_final: 0.3221 (p0)
REVERT: A  405 ASN cc_start: 0.8541 (p0) cc_final: 0.8213 (p0)
REVERT: D   37 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6991 (mt-10)
REVERT: D   68 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7679 (ttmm)
REVERT: D  295 ASP cc_start: 0.6833 (p0) cc_final: 0.6582 (m-30)
REVERT: D  347 THR cc_start: 0.7964 (m) cc_final: 0.7688 (p)
REVERT: D  376 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7831 (mtt)
REVERT: D  518 ARG cc_start: 0.8339 (tmm160) cc_final: 0.8034 (ttp80)
REVERT: D  555 PHE cc_start: 0.8356 (t80) cc_final: 0.7965 (t80)
REVERT: D  556 ASN cc_start: 0.8111 (m-40) cc_final: 0.7581 (m-40)
REVERT: D  613 TYR cc_start: 0.6834 (p90) cc_final: 0.6395 (p90)
  outliers start: 22
  outliers final: 8
  residues processed: 175
  average time/residue: 1.1551
  time to fit residues: 212.8676
Evaluate side-chains
  158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  254 SER
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  445 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9980
   chunk 61 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN
D 239 HIS
D 305 GLN
D 345 HIS
D 373 HIS
D 578 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.139236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.124147 restraints weight = 9342.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.03
r_work: 0.3487 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6671  Z= 0.183
  Angle     :  0.582   8.336   9071  Z= 0.295
  Chirality :  0.044   0.164    953
  Planarity :  0.004   0.039   1172
  Dihedral  :  3.869  21.827    925
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.26 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.30), residues: 789
  helix:  0.57 (0.26), residues: 404
  sheet: -0.77 (0.76), residues: 43
  loop : -1.01 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 349 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.015   0.002   PHE D 285 
 TYR   0.018   0.002   TYR A 396 
 ARG   0.005   0.001   ARG D 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00261 (    3)
  link_NAG-ASN         : angle       3.51490 (    9)
  hydrogen bonds       : bond        0.05095 (  300)
  hydrogen bonds       : angle       4.48106 (  846)
  metal coordination   : bond        0.00358 (    1)
  SS BOND              : bond        0.00448 (    1)
  SS BOND              : angle       0.48421 (    2)
  covalent geometry    : bond        0.00421 ( 6666)
  covalent geometry    : angle       0.57152 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8472 (p0) cc_final: 0.8215 (p0)
REVERT: A  408 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8250 (m)
REVERT: D   75 GLU cc_start: 0.7570 (pt0) cc_final: 0.7330 (pt0)
REVERT: D  114 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7565 (mmmt)
REVERT: D  131 LYS cc_start: 0.7487 (ttmm) cc_final: 0.7136 (tppt)
REVERT: D  295 ASP cc_start: 0.7035 (p0) cc_final: 0.6735 (t0)
REVERT: D  347 THR cc_start: 0.8116 (m) cc_final: 0.7881 (p)
REVERT: D  470 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8352 (ttpp)
REVERT: D  518 ARG cc_start: 0.8345 (tmm160) cc_final: 0.8053 (ttp80)
REVERT: D  541 LYS cc_start: 0.7590 (mttm) cc_final: 0.7372 (mttp)
REVERT: D  556 ASN cc_start: 0.8167 (m-40) cc_final: 0.7840 (m-40)
REVERT: D  589 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7442 (tp30)
REVERT: D  613 TYR cc_start: 0.7347 (p90) cc_final: 0.6759 (p90)
  outliers start: 26
  outliers final: 10
  residues processed: 174
  average time/residue: 1.2186
  time to fit residues: 223.4608
Evaluate side-chains
  158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  424 LEU
Chi-restraints excluded: chain D residue  445 THR
Chi-restraints excluded: chain D residue  470 LYS
Chi-restraints excluded: chain D residue  589 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 25 optimal weight:    0.1980
   chunk 64 optimal weight:    0.4980
   chunk 37 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
A 439 ASN
A 477 ASN
D  96 GLN
D 300 GLN
D 330 ASN
D 401 HIS
D 578 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.138479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.123451 restraints weight = 9331.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.03
r_work: 0.3476 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6671  Z= 0.172
  Angle     :  0.589  11.304   9071  Z= 0.290
  Chirality :  0.043   0.139    953
  Planarity :  0.004   0.040   1172
  Dihedral  :  3.884  17.089    925
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.40 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.30), residues: 789
  helix:  0.74 (0.26), residues: 399
  sheet: -0.80 (0.73), residues: 43
  loop : -0.93 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 168 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.018   0.002   PHE D 285 
 TYR   0.022   0.002   TYR D  50 
 ARG   0.004   0.000   ARG D 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00101 (    3)
  link_NAG-ASN         : angle       3.23993 (    9)
  hydrogen bonds       : bond        0.04996 (  300)
  hydrogen bonds       : angle       4.53242 (  846)
  metal coordination   : bond        0.00464 (    1)
  SS BOND              : bond        0.00403 (    1)
  SS BOND              : angle       0.39823 (    2)
  covalent geometry    : bond        0.00405 ( 6666)
  covalent geometry    : angle       0.58005 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8418 (p0) cc_final: 0.8181 (p0)
REVERT: D   75 GLU cc_start: 0.7616 (pt0) cc_final: 0.7367 (pt0)
REVERT: D   81 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7790 (mm-40)
REVERT: D  114 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7525 (mmmt)
REVERT: D  131 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7523 (tppt)
REVERT: D  249 MET cc_start: 0.7844 (mpp) cc_final: 0.7607 (mmt)
REVERT: D  267 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8322 (mt)
REVERT: D  470 LYS cc_start: 0.8655 (tppp) cc_final: 0.8379 (ttpp)
REVERT: D  518 ARG cc_start: 0.8355 (tmm160) cc_final: 0.8076 (ttp80)
REVERT: D  556 ASN cc_start: 0.8247 (m-40) cc_final: 0.7709 (m110)
REVERT: D  613 TYR cc_start: 0.7492 (p90) cc_final: 0.6967 (p90)
  outliers start: 26
  outliers final: 13
  residues processed: 172
  average time/residue: 1.3973
  time to fit residues: 253.1044
Evaluate side-chains
  163 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  254 SER
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  280 SER
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  435 GLU
Chi-restraints excluded: chain D residue  445 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.0980
   chunk 25 optimal weight:    0.0570
   chunk 24 optimal weight:    0.1980
   chunk 40 optimal weight:    0.4980
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0770
   chunk 8 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.1256

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

Flipped N/Q/H residues before XYZ refinement:
D 210 ASN
D 378 HIS
D 401 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124703 restraints weight = 9322.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.96
r_work: 0.3513 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6671  Z= 0.110
  Angle     :  0.518   7.333   9071  Z= 0.260
  Chirality :  0.040   0.124    953
  Planarity :  0.004   0.041   1172
  Dihedral  :  3.547  13.151    925
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.70 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.30), residues: 789
  helix:  0.97 (0.27), residues: 399
  sheet: -0.66 (0.74), residues: 43
  loop : -0.84 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 168 
 HIS   0.005   0.001   HIS D 374 
 PHE   0.020   0.001   PHE D 285 
 TYR   0.018   0.001   TYR D  50 
 ARG   0.004   0.000   ARG D 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00057 (    3)
  link_NAG-ASN         : angle       2.79626 (    9)
  hydrogen bonds       : bond        0.04282 (  300)
  hydrogen bonds       : angle       4.42387 (  846)
  metal coordination   : bond        0.00144 (    1)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       0.02693 (    2)
  covalent geometry    : bond        0.00243 ( 6666)
  covalent geometry    : angle       0.51047 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8429 (p0) cc_final: 0.8121 (p0)
REVERT: A  408 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8278 (m)
REVERT: D   37 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7110 (mp0)
REVERT: D   43 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8638 (p)
REVERT: D   75 GLU cc_start: 0.7563 (pt0) cc_final: 0.7355 (pt0)
REVERT: D  114 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7570 (mmmm)
REVERT: D  518 ARG cc_start: 0.8331 (tmm160) cc_final: 0.8088 (ttp80)
REVERT: D  556 ASN cc_start: 0.8209 (m-40) cc_final: 0.7694 (m110)
REVERT: D  577 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8006 (mtpp)
REVERT: D  613 TYR cc_start: 0.7447 (p90) cc_final: 0.6972 (p90)
  outliers start: 18
  outliers final: 9
  residues processed: 174
  average time/residue: 1.2503
  time to fit residues: 227.8747
Evaluate side-chains
  162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  445 THR
Chi-restraints excluded: chain D residue  476 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0010
   chunk 75 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0770
   chunk 31 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.3144

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

Flipped N/Q/H residues before XYZ refinement:
D 401 HIS
D 522 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.137864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.122923 restraints weight = 9083.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.98
r_work: 0.3474 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6671  Z= 0.165
  Angle     :  0.560   6.874   9071  Z= 0.285
  Chirality :  0.043   0.131    953
  Planarity :  0.004   0.042   1172
  Dihedral  :  3.874  17.548    925
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.99 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.30), residues: 789
  helix:  0.99 (0.27), residues: 399
  sheet: -0.63 (0.73), residues: 43
  loop : -0.87 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 168 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.024   0.002   PHE D 285 
 TYR   0.016   0.001   TYR A 369 
 ARG   0.004   0.000   ARG D 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00183 (    3)
  link_NAG-ASN         : angle       3.06414 (    9)
  hydrogen bonds       : bond        0.04920 (  300)
  hydrogen bonds       : angle       4.47430 (  846)
  metal coordination   : bond        0.00364 (    1)
  SS BOND              : bond        0.00403 (    1)
  SS BOND              : angle       0.53681 (    2)
  covalent geometry    : bond        0.00391 ( 6666)
  covalent geometry    : angle       0.55173 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.8405 (p0) cc_final: 0.8111 (p0)
REVERT: A  408 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8282 (m)
REVERT: D   37 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7344 (mp0)
REVERT: D   43 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8615 (p)
REVERT: D   75 GLU cc_start: 0.7541 (pt0) cc_final: 0.7257 (pt0)
REVERT: D  114 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7574 (mmmm)
REVERT: D  142 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6293 (pp)
REVERT: D  410 LEU cc_start: 0.7637 (tp) cc_final: 0.7434 (mt)
REVERT: D  518 ARG cc_start: 0.8336 (tmm160) cc_final: 0.8088 (ttp80)
REVERT: D  556 ASN cc_start: 0.8233 (m-40) cc_final: 0.7746 (m110)
REVERT: D  577 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8076 (mtpp)
REVERT: D  613 TYR cc_start: 0.7586 (p90) cc_final: 0.7063 (p90)
  outliers start: 20
  outliers final: 10
  residues processed: 169
  average time/residue: 1.1833
  time to fit residues: 209.9265
Evaluate side-chains
  158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  424 LEU
Chi-restraints excluded: chain D residue  445 THR
Chi-restraints excluded: chain D residue  476 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    0.0570
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0980
   chunk 0 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0670
   chunk 42 optimal weight:    0.0000
   overall best weight:    0.1640

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

Flipped N/Q/H residues before XYZ refinement:
D 210 ASN
D 442 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.140037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.124902 restraints weight = 9145.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 1.99
r_work: 0.3498 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6671  Z= 0.122
  Angle     :  0.535   8.563   9071  Z= 0.269
  Chirality :  0.041   0.128    953
  Planarity :  0.004   0.042   1172
  Dihedral  :  3.765  17.474    925
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.85 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.30), residues: 789
  helix:  1.13 (0.27), residues: 399
  sheet: -0.44 (0.74), residues: 43
  loop : -0.76 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP D 168 
 HIS   0.005   0.001   HIS D 374 
 PHE   0.023   0.001   PHE D 285 
 TYR   0.019   0.001   TYR D  50 
 ARG   0.009   0.000   ARG D 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00100 (    3)
  link_NAG-ASN         : angle       2.47494 (    9)
  hydrogen bonds       : bond        0.04400 (  300)
  hydrogen bonds       : angle       4.43115 (  846)
  metal coordination   : bond        0.00154 (    1)
  SS BOND              : bond        0.00242 (    1)
  SS BOND              : angle       0.14897 (    2)
  covalent geometry    : bond        0.00278 ( 6666)
  covalent geometry    : angle       0.52944 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 155
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 CYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6807 (m)
REVERT: A  405 ASN cc_start: 0.8394 (p0) cc_final: 0.8074 (p0)
REVERT: A  408 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8285 (m)
REVERT: D   43 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8644 (p)
REVERT: D   75 GLU cc_start: 0.7582 (pt0) cc_final: 0.7288 (pt0)
REVERT: D  114 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7596 (mmmt)
REVERT: D  142 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5809 (pp)
REVERT: D  152 MET cc_start: 0.7650 (mmm) cc_final: 0.7421 (mmp)
REVERT: D  267 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8298 (mt)
REVERT: D  349 TRP cc_start: 0.8594 (m100) cc_final: 0.8282 (m100)
REVERT: D  518 ARG cc_start: 0.8369 (tmm160) cc_final: 0.8140 (ttp80)
REVERT: D  556 ASN cc_start: 0.8260 (m-40) cc_final: 0.7808 (m110)
REVERT: D  577 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8066 (mtpp)
REVERT: D  613 TYR cc_start: 0.7563 (p90) cc_final: 0.7087 (p90)
  outliers start: 22
  outliers final: 12
  residues processed: 172
  average time/residue: 1.1180
  time to fit residues: 202.4936
Evaluate side-chains
  168 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  248 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  280 SER
Chi-restraints excluded: chain D residue  325 GLN
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  445 THR
Chi-restraints excluded: chain D residue  476 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 14 optimal weight:    0.3980
   chunk 51 optimal weight:    0.4980
   chunk 29 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 66 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0010
   chunk 77 optimal weight:    0.1980
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.2986

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN
D 401 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.137752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122737 restraints weight = 9079.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.99
r_work: 0.3461 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6671  Z= 0.163
  Angle     :  0.566   7.508   9071  Z= 0.286
  Chirality :  0.043   0.179    953
  Planarity :  0.004   0.042   1172
  Dihedral  :  3.901  15.571    925
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.99 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.30), residues: 789
  helix:  1.07 (0.27), residues: 399
  sheet: -0.46 (0.73), residues: 43
  loop : -0.85 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 168 
 HIS   0.008   0.001   HIS D 374 
 PHE   0.025   0.002   PHE D 285 
 TYR   0.017   0.002   TYR A 369 
 ARG   0.005   0.000   ARG D 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00119 (    3)
  link_NAG-ASN         : angle       2.61851 (    9)
  hydrogen bonds       : bond        0.04963 (  300)
  hydrogen bonds       : angle       4.49666 (  846)
  metal coordination   : bond        0.00292 (    1)
  SS BOND              : bond        0.00358 (    1)
  SS BOND              : angle       0.67551 (    2)
  covalent geometry    : bond        0.00384 ( 6666)
  covalent geometry    : angle       0.55984 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 CYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6839 (m)
REVERT: A  405 ASN cc_start: 0.8397 (p0) cc_final: 0.8081 (p0)
REVERT: A  408 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8295 (m)
REVERT: D   37 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7302 (mp0)
REVERT: D   43 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8610 (p)
REVERT: D   75 GLU cc_start: 0.7557 (pt0) cc_final: 0.7277 (pt0)
REVERT: D  114 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7584 (mmmt)
REVERT: D  152 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7490 (mmp)
REVERT: D  267 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8391 (mt)
REVERT: D  349 TRP cc_start: 0.8606 (m100) cc_final: 0.8332 (m100)
REVERT: D  406 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7609 (mm-30)
REVERT: D  410 LEU cc_start: 0.7618 (tp) cc_final: 0.7418 (mt)
REVERT: D  411 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7829 (m)
REVERT: D  518 ARG cc_start: 0.8351 (tmm160) cc_final: 0.8065 (ttp80)
REVERT: D  556 ASN cc_start: 0.8237 (m-40) cc_final: 0.7804 (m-40)
REVERT: D  577 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8088 (mtpp)
REVERT: D  613 TYR cc_start: 0.7606 (p90) cc_final: 0.7118 (p90)
  outliers start: 20
  outliers final: 10
  residues processed: 168
  average time/residue: 1.3320
  time to fit residues: 237.1200
Evaluate side-chains
  160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  152 MET
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  248 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  445 THR
Chi-restraints excluded: chain D residue  476 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0870
   chunk 9 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:    0.2980
   chunk 68 optimal weight:    0.0670
   chunk 4 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0980
   overall best weight:    0.1696

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

Flipped N/Q/H residues before XYZ refinement:
D 210 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.139620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.124587 restraints weight = 9285.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.01
r_work: 0.3484 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6671  Z= 0.123
  Angle     :  0.548   8.158   9071  Z= 0.275
  Chirality :  0.041   0.136    953
  Planarity :  0.004   0.042   1172
  Dihedral  :  3.732  13.274    925
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 24.14 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.30), residues: 789
  helix:  1.16 (0.27), residues: 396
  sheet: -0.40 (0.73), residues: 43
  loop : -0.78 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP D 168 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.026   0.001   PHE D 285 
 TYR   0.025   0.001   TYR D  50 
 ARG   0.006   0.000   ARG D 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00118 (    3)
  link_NAG-ASN         : angle       2.37302 (    9)
  hydrogen bonds       : bond        0.04492 (  300)
  hydrogen bonds       : angle       4.46213 (  846)
  metal coordination   : bond        0.00176 (    1)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       0.33294 (    2)
  covalent geometry    : bond        0.00279 ( 6666)
  covalent geometry    : angle       0.54333 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 CYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6761 (m)
REVERT: A  405 ASN cc_start: 0.8391 (p0) cc_final: 0.8079 (p0)
REVERT: A  408 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8268 (m)
REVERT: D   37 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7254 (mp0)
REVERT: D   43 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8653 (p)
REVERT: D   75 GLU cc_start: 0.7586 (pt0) cc_final: 0.7281 (pt0)
REVERT: D  114 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7670 (mmmt)
REVERT: D  117 ASN cc_start: 0.8224 (m-40) cc_final: 0.8019 (m-40)
REVERT: D  210 ASN cc_start: 0.7800 (m-40) cc_final: 0.7539 (m-40)
REVERT: D  267 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8379 (mt)
REVERT: D  349 TRP cc_start: 0.8579 (m100) cc_final: 0.8303 (m100)
REVERT: D  410 LEU cc_start: 0.7531 (tp) cc_final: 0.7307 (mt)
REVERT: D  518 ARG cc_start: 0.8362 (tmm160) cc_final: 0.8138 (ttp80)
REVERT: D  556 ASN cc_start: 0.8213 (m-40) cc_final: 0.7766 (m110)
REVERT: D  577 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8062 (mtpp)
REVERT: D  613 TYR cc_start: 0.7573 (p90) cc_final: 0.7109 (p90)
  outliers start: 20
  outliers final: 11
  residues processed: 162
  average time/residue: 1.2223
  time to fit residues: 210.2520
Evaluate side-chains
  162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 1.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  248 LEU
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  325 GLN
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  445 THR
Chi-restraints excluded: chain D residue  476 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0870
   chunk 41 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0040
   chunk 8 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.4980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.1546

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.140142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125009 restraints weight = 9240.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.01
r_work: 0.3488 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6671  Z= 0.121
  Angle     :  0.548   8.528   9071  Z= 0.276
  Chirality :  0.041   0.131    953
  Planarity :  0.004   0.041   1172
  Dihedral  :  3.627  13.116    925
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 25.14 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.30), residues: 789
  helix:  1.16 (0.27), residues: 396
  sheet: -0.32 (0.74), residues: 43
  loop : -0.72 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP D 168 
 HIS   0.005   0.001   HIS D 374 
 PHE   0.024   0.001   PHE D 285 
 TYR   0.017   0.001   TYR A 369 
 ARG   0.008   0.000   ARG D 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    3)
  link_NAG-ASN         : angle       2.28690 (    9)
  hydrogen bonds       : bond        0.04468 (  300)
  hydrogen bonds       : angle       4.44989 (  846)
  metal coordination   : bond        0.00156 (    1)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.39634 (    2)
  covalent geometry    : bond        0.00273 ( 6666)
  covalent geometry    : angle       0.54370 ( 9060)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 CYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6764 (m)
REVERT: A  405 ASN cc_start: 0.8391 (p0) cc_final: 0.8065 (p0)
REVERT: A  408 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8256 (m)
REVERT: D   37 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7219 (mp0)
REVERT: D   43 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8647 (p)
REVERT: D   75 GLU cc_start: 0.7590 (pt0) cc_final: 0.7285 (pt0)
REVERT: D  349 TRP cc_start: 0.8559 (m100) cc_final: 0.8273 (m100)
REVERT: D  518 ARG cc_start: 0.8363 (tmm160) cc_final: 0.8133 (ttp80)
REVERT: D  556 ASN cc_start: 0.8149 (m-40) cc_final: 0.7731 (m110)
REVERT: D  577 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8036 (mtpp)
REVERT: D  613 TYR cc_start: 0.7554 (p90) cc_final: 0.7075 (p90)
  outliers start: 15
  outliers final: 10
  residues processed: 165
  average time/residue: 1.8684
  time to fit residues: 326.6235
Evaluate side-chains
  160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 1.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  325 GLN
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  411 SER
Chi-restraints excluded: chain D residue  445 THR
Chi-restraints excluded: chain D residue  476 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.1980
   chunk 31 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0870
   chunk 48 optimal weight:    0.3980
   chunk 49 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0070
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.1554

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.125028 restraints weight = 9294.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.01
r_work: 0.3491 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6671  Z= 0.121
  Angle     :  0.548   6.488   9071  Z= 0.277
  Chirality :  0.041   0.134    953
  Planarity :  0.004   0.042   1172
  Dihedral  :  3.617  13.262    925
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 25.29 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.30), residues: 789
  helix:  1.13 (0.26), residues: 397
  sheet: -0.31 (0.74), residues: 43
  loop : -0.66 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP D 168 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.024   0.001   PHE D 285 
 TYR   0.030   0.001   TYR D  50 
 ARG   0.009   0.000   ARG D 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00121 (    3)
  link_NAG-ASN         : angle       2.25201 (    9)
  hydrogen bonds       : bond        0.04451 (  300)
  hydrogen bonds       : angle       4.45393 (  846)
  metal coordination   : bond        0.00160 (    1)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.36441 (    2)
  covalent geometry    : bond        0.00274 ( 6666)
  covalent geometry    : angle       0.54351 ( 9060)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7762.22 seconds
wall clock time: 138 minutes 56.62 seconds (8336.62 seconds total)