Starting phenix.real_space_refine
on Fri Aug 22 17:50:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aqs_15588/08_2025/8aqs_15588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aqs_15588/08_2025/8aqs_15588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aqs_15588/08_2025/8aqs_15588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aqs_15588/08_2025/8aqs_15588.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aqs_15588/08_2025/8aqs_15588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aqs_15588/08_2025/8aqs_15588.map"
  }
  resolution = 2.92
  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=  -0.000 sd=   0.030
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4155      2.51       5
     N    1073      2.21       5
     O    1227      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6493
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1543
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 4864
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
      Conformer: "C"
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
          bond proxies already assigned to first conformer: 4985
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 72
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6, 'water': 1}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 2.67, per 1000 atoms: 0.41
  Number of scatterers: 6493
  At special positions: 0
  Unit cell: (89.2672, 78.1088, 118.685, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1227      8.00
     N    1073      7.00
     C    4155      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG B 901 " - " ASN B  53 "
      " NAG B 902 " - " ASN B  90 "
      " NAG B 903 " - " ASN B 103 "
      " NAG B 904 " - " ASN B 546 "
      " NAG B 905 " - " ASN B 322 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 439.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 906 "
        pdb="ZN    ZN B 906 " - pdb=" NE2 HIS B 374 "
        pdb="ZN    ZN B 906 " - pdb=" NE2 HIS B 378 "


  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      53.7% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.105A  pdb=" N   PHE A 371 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.662A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 506
      removed outlier: 3.902A  pdb=" N   GLN A 506 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 53
      removed outlier: 3.945A  pdb=" N   TYR B  41 " --> pdb=" O   GLU B  37 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLN B  42 " --> pdb=" O   ASP B  38 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER B  43 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 81
    Processing helix  chain 'B' and resid 90 through 101
    Processing helix  chain 'B' and resid 109 through 130
    Processing helix  chain 'B' and resid 147 through 154
    Processing helix  chain 'B' and resid 157 through 194
      removed outlier: 3.663A  pdb=" N   ARG B 161 " --> pdb=" O   ASP B 157 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   GLN B 175 " --> pdb=" O   GLU B 171 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU B 176 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ARG B 177 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 220 through 252
      removed outlier: 4.068A  pdb=" N   GLU B 224 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLU B 232 " --> pdb=" O   HIS B 228 " (cutoff:3.500A)
      Proline residue:  B 235  - end of helix
    Processing helix  chain 'B' and resid 265 through 267
      No H-bonds generated for 'chain 'B' and resid 265 through 267'
    Processing helix  chain 'B' and resid 275 through 279
      removed outlier: 3.739A  pdb=" N   TYR B 279 " --> pdb=" O   THR B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 303 through 311
      removed outlier: 3.599A  pdb=" N   ALA B 311 " --> pdb=" O   ILE B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 319
      removed outlier: 3.505A  pdb=" N   VAL B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 331
      removed outlier: 4.166A  pdb=" N   TRP B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLU B 329 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 385
      removed outlier: 3.889A  pdb=" N   PHE B 369 " --> pdb=" O   THR B 365 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 370 " --> pdb=" O   MET B 366 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TYR B 385 " --> pdb=" O   TYR B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 393
      removed outlier: 3.528A  pdb=" N   ARG B 393 " --> pdb=" O   PHE B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 412
      removed outlier: 3.664A  pdb=" N   SER B 411 " --> pdb=" O   ILE B 407 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ALA B 412 " --> pdb=" O   MET B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 421
    Processing helix  chain 'B' and resid 431 through 444
      removed outlier: 3.903A  pdb=" N   ILE B 436 " --> pdb=" O   ASN B 432 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ASN B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 466
    Processing helix  chain 'B' and resid 469 through 471
      No H-bonds generated for 'chain 'B' and resid 469 through 471'
    Processing helix  chain 'B' and resid 472 through 484
      removed outlier: 3.654A  pdb=" N   ARG B 482 " --> pdb=" O   TRP B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 502
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.590A  pdb=" N   SER B 507 " --> pdb=" O   LEU B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 533
      removed outlier: 3.645A  pdb=" N   THR B 517 " --> pdb=" O   ILE B 513 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   THR B 519 " --> pdb=" O   TYR B 515 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 547 through 559
      removed outlier: 3.980A  pdb=" N   GLY B 551 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   MET B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 574
    Processing helix  chain 'B' and resid 581 through 599
      Proline residue:  B 590  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    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
    Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 263
      removed outlier: 6.112A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 352
      removed outlier: 6.053A  pdb=" N   ASP B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    818 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2074
        1.34 -     1.46: 1675
        1.46 -     1.58: 2869
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6676
  Sorted by residual:
  bond pdb=" C1  NAG B 902 "
       pdb=" O5  NAG B 902 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.06e+00
  bond pdb=" C1  NAG B 904 "
       pdb=" O5  NAG B 904 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.74e+00
  bond pdb=" C1  NAG B 903 "
       pdb=" O5  NAG B 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.74e+00
  bond pdb=" C1  NAG B 901 "
       pdb=" O5  NAG B 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.66e+00
  bond pdb=" C5  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.40e+00
  ... (remaining 6671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 8959
        2.07 -     4.13: 102
        4.13 -     6.20: 13
        6.20 -     8.26: 1
        8.26 -    10.33: 1
  Bond angle restraints: 9076
  Sorted by residual:
  angle pdb=" C   PHE A 371 "
        pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
      ideal   model   delta    sigma   weight residual
     121.80  132.13  -10.33 2.44e+00 1.68e-01 1.79e+01
  angle pdb=" C   PRO B  84 "
        pdb=" N   LEU B  85 "
        pdb=" CA  LEU B  85 "
      ideal   model   delta    sigma   weight residual
     121.54  127.71   -6.17 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" N   ILE A 418 "
        pdb=" CA  ILE A 418 "
        pdb=" C   ILE A 418 "
      ideal   model   delta    sigma   weight residual
     111.81  109.22    2.59 8.60e-01 1.35e+00 9.08e+00
  angle pdb=" N   LYS B 174 "
        pdb=" CA  LYS B 174 "
        pdb=" C   LYS B 174 "
      ideal   model   delta    sigma   weight residual
     112.72  109.37    3.35 1.14e+00 7.69e-01 8.64e+00
  angle pdb=" N   GLN B 175 "
        pdb=" CA  GLN B 175 "
        pdb=" C   GLN B 175 "
      ideal   model   delta    sigma   weight residual
     114.64  110.19    4.45 1.52e+00 4.33e-01 8.55e+00
  ... (remaining 9071 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.81: 3737
       21.81 -    43.62: 229
       43.62 -    65.43: 25
       65.43 -    87.24: 9
       87.24 -   109.05: 8
  Dihedral angle restraints: 4008
    sinusoidal: 1689
      harmonic: 2319
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.82  -34.82     1      1.00e+01 1.00e-02 1.72e+01
  dihedral pdb=" C1  NAG B 905 "
           pdb=" C2  NAG B 905 "
           pdb=" C3  NAG B 905 "
           pdb=" O3  NAG B 905 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -66.04 -109.05     1      3.00e+01 1.11e-03 1.41e+01
  dihedral pdb=" C1  NAG B 905 "
           pdb=" C2  NAG B 905 "
           pdb=" C3  NAG B 905 "
           pdb=" C4  NAG B 905 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.39   55.85 -108.24     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 4005 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 897
       0.081 -    0.163: 66
       0.163 -    0.244: 0
       0.244 -    0.325: 0
       0.325 -    0.406: 1
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" CB  ILE B 407 "
            pdb=" CA  ILE B 407 "
            pdb=" CG1 ILE B 407 "
            pdb=" CG2 ILE B 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" C1  NAG B 904 "
            pdb=" ND2 ASN B 546 "
            pdb=" C2  NAG B 904 "
            pdb=" O5  NAG B 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 961 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 145 "   -0.037 5.00e-02 4.00e+02   5.55e-02 4.93e+00
        pdb=" N   PRO B 146 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 146 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 146 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 234 "    0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO B 235 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 235 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 235 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 293 "   -0.006 2.00e-02 2.50e+03   1.28e-02 1.64e+00
        pdb=" C   VAL B 293 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL B 293 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   THR B 294 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 996
        2.76 -     3.30: 5887
        3.30 -     3.83: 10338
        3.83 -     4.37: 12079
        4.37 -     4.90: 21510
  Nonbonded interactions: 50810
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" O   ILE B 358 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" NE  ARG A 457 "
            pdb=" OD2 ASP A 467 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" OG  SER A 438 "
            pdb=" OD2 ASP A 442 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.369 3.040
  ... (remaining 50805 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=0.40 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:             3.300
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.610
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.870
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
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   0.030   6688  Z= 0.132
  Angle     :  0.560  10.326   9102  Z= 0.295
  Chirality :  0.043   0.406    964
  Planarity :  0.004   0.055   1170
  Dihedral  : 14.740 109.048   2508
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.93 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.31), residues: 785
  helix:  1.81 (0.29), residues: 357
  sheet:  1.33 (0.79), residues: 45
  loop : -0.97 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.020   0.001   TYR A 501 
 PHE   0.018   0.001   PHE B 400 
 TRP   0.013   0.001   TRP B 477 
 HIS   0.003   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6676)
  covalent geometry    : angle       0.54345 ( 9076)
  SS BOND              : bond        0.00134 (    4)
  SS BOND              : angle       0.54890 (    8)
  hydrogen bonds       : bond        0.15023 (  292)
  hydrogen bonds       : angle       4.79337 (  818)
  metal coordination   : bond        0.00079 (    2)
  link_NAG-ASN         : bond        0.00640 (    6)
  link_NAG-ASN         : angle       3.04197 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  440 LYS cc_start: 0.8615 (mttm) cc_final: 0.8305 (mmtm)
REVERT: A  444 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8226 (mtpm)
REVERT: A  467 ASP cc_start: 0.8491 (t0) cc_final: 0.8133 (t0)
REVERT: B   60 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7522 (mm-40)
REVERT: B   89 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8120 (mm-40)
REVERT: B  102 GLN cc_start: 0.7907 (pt0) cc_final: 0.7402 (mm110)
REVERT: B  131 LYS cc_start: 0.7573 (ptmm) cc_final: 0.7283 (tttm)
REVERT: B  150 GLU cc_start: 0.7073 (tp30) cc_final: 0.6606 (mp0)
REVERT: B  190 MET cc_start: 0.7201 (tmm) cc_final: 0.6966 (tmm)
REVERT: B  213 ASP cc_start: 0.6790 (p0) cc_final: 0.6510 (t0)
REVERT: B  270 MET cc_start: 0.6371 (tpp) cc_final: 0.6046 (mmm)
REVERT: B  397 ASN cc_start: 0.8226 (p0) cc_final: 0.7972 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.5964
  time to fit residues: 70.7204
Evaluate side-chains
  81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
B  34 HIS    C
B 325 GLN
B 401 HIS
B 472 GLN
B 552 GLN
B 598 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.155071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121405 restraints weight = 14030.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 3.76
r_work: 0.3085 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6688  Z= 0.182
  Angle     :  0.635  10.089   9102  Z= 0.322
  Chirality :  0.046   0.383    964
  Planarity :  0.005   0.051   1170
  Dihedral  :  8.239  74.473    985
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.95 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.24 %
    Favored  : 89.18 %
  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 aren not related in a simple way.
  whole:  0.47 (0.30), residues: 785
  helix:  1.44 (0.28), residues: 370
  sheet:  0.79 (0.69), residues: 55
  loop : -0.97 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 357 
 TYR   0.025   0.002   TYR B 183 
 PHE   0.035   0.002   PHE B 400 
 TRP   0.009   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 6676)
  covalent geometry    : angle       0.61829 ( 9076)
  SS BOND              : bond        0.00341 (    4)
  SS BOND              : angle       1.56574 (    8)
  hydrogen bonds       : bond        0.06577 (  292)
  hydrogen bonds       : angle       4.37617 (  818)
  metal coordination   : bond        0.00281 (    2)
  link_NAG-ASN         : bond        0.00629 (    6)
  link_NAG-ASN         : angle       3.19507 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  440 LYS cc_start: 0.8720 (mttm) cc_final: 0.8377 (mmtm)
REVERT: A  444 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8247 (mtpm)
REVERT: A  458 LYS cc_start: 0.7591 (ptmt) cc_final: 0.7385 (ptmt)
REVERT: B  131 LYS cc_start: 0.7464 (ptmm) cc_final: 0.7254 (tttm)
REVERT: B  150 GLU cc_start: 0.6914 (tp30) cc_final: 0.6540 (mp0)
REVERT: B  332 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8194 (ttp)
  outliers start: 11
  outliers final: 2
  residues processed: 97
  average time/residue: 0.5836
  time to fit residues: 59.6451
Evaluate side-chains
  88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.155845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120166 restraints weight = 9810.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.37
r_work: 0.3171 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6688  Z= 0.147
  Angle     :  0.608  10.234   9102  Z= 0.303
  Chirality :  0.044   0.387    964
  Planarity :  0.004   0.049   1170
  Dihedral  :  6.807  54.836    985
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.83 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.83 %
    Favored  : 86.44 %
  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 aren not related in a simple way.
  whole:  0.53 (0.30), residues: 785
  helix:  1.54 (0.28), residues: 364
  sheet:  0.73 (0.68), residues: 55
  loop : -0.96 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 357 
 TYR   0.023   0.002   TYR B 183 
 PHE   0.024   0.001   PHE B 400 
 TRP   0.010   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6676)
  covalent geometry    : angle       0.58999 ( 9076)
  SS BOND              : bond        0.00329 (    4)
  SS BOND              : angle       1.37542 (    8)
  hydrogen bonds       : bond        0.05708 (  292)
  hydrogen bonds       : angle       4.23924 (  818)
  metal coordination   : bond        0.00195 (    2)
  link_NAG-ASN         : bond        0.00695 (    6)
  link_NAG-ASN         : angle       3.26482 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7532 (ptm160)
REVERT: A  440 LYS cc_start: 0.8725 (mttm) cc_final: 0.8389 (mmtm)
REVERT: A  444 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8306 (mtpm)
REVERT: B  332 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8093 (ttt)
  outliers start: 12
  outliers final: 6
  residues processed: 92
  average time/residue: 0.5583
  time to fit residues: 54.1376
Evaluate side-chains
  84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  332 MET
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.156905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.120999 restraints weight = 9502.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.25
r_work: 0.3189 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6688  Z= 0.137
  Angle     :  0.595  10.247   9102  Z= 0.294
  Chirality :  0.044   0.387    964
  Planarity :  0.004   0.050   1170
  Dihedral  :  6.111  54.710    985
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.83 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.41 %
    Favored  : 85.43 %
  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 aren not related in a simple way.
  whole:  0.55 (0.30), residues: 785
  helix:  1.55 (0.28), residues: 364
  sheet:  0.78 (0.67), residues: 55
  loop : -0.93 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 357 
 TYR   0.019   0.001   TYR B  50 
 PHE   0.020   0.001   PHE B 400 
 TRP   0.009   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6676)
  covalent geometry    : angle       0.57629 ( 9076)
  SS BOND              : bond        0.00309 (    4)
  SS BOND              : angle       1.39884 (    8)
  hydrogen bonds       : bond        0.05399 (  292)
  hydrogen bonds       : angle       4.12410 (  818)
  metal coordination   : bond        0.00175 (    2)
  link_NAG-ASN         : bond        0.00661 (    6)
  link_NAG-ASN         : angle       3.28250 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7540 (ptm160)
REVERT: A  440 LYS cc_start: 0.8723 (mttm) cc_final: 0.8411 (mmtm)
REVERT: B  341 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7184 (mmmt)
  outliers start: 15
  outliers final: 9
  residues processed: 92
  average time/residue: 0.5673
  time to fit residues: 55.1252
Evaluate side-chains
  87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0020
   chunk 68 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    1.0792

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.153352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116508 restraints weight = 9966.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.44
r_work: 0.3149 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6688  Z= 0.159
  Angle     :  0.615  10.191   9102  Z= 0.306
  Chirality :  0.045   0.393    964
  Planarity :  0.004   0.049   1170
  Dihedral  :  5.947  55.741    985
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.34 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.00 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.30), residues: 785
  helix:  1.49 (0.27), residues: 364
  sheet:  0.90 (0.68), residues: 55
  loop : -0.98 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.016   0.002   TYR A 501 
 PHE   0.023   0.001   PHE B 400 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.005   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6676)
  covalent geometry    : angle       0.59742 ( 9076)
  SS BOND              : bond        0.00259 (    4)
  SS BOND              : angle       1.45704 (    8)
  hydrogen bonds       : bond        0.05929 (  292)
  hydrogen bonds       : angle       4.15371 (  818)
  metal coordination   : bond        0.00344 (    2)
  link_NAG-ASN         : bond        0.00652 (    6)
  link_NAG-ASN         : angle       3.25232 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  346 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7496 (ptm160)
REVERT: A  440 LYS cc_start: 0.8775 (mttm) cc_final: 0.8412 (mmtm)
REVERT: B  341 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7181 (mmmt)
  outliers start: 15
  outliers final: 11
  residues processed: 88
  average time/residue: 0.5984
  time to fit residues: 55.3727
Evaluate side-chains
  84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.156287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116402 restraints weight = 18475.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.82
r_work: 0.3138 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6688  Z= 0.136
  Angle     :  0.591  10.249   9102  Z= 0.291
  Chirality :  0.043   0.392    964
  Planarity :  0.004   0.048   1170
  Dihedral  :  5.619  55.072    985
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.95 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.29 %
    Favored  : 83.55 %
  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 aren not related in a simple way.
  whole:  0.59 (0.30), residues: 785
  helix:  1.59 (0.28), residues: 364
  sheet:  0.79 (0.68), residues: 55
  loop : -0.93 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 501 
 PHE   0.016   0.001   PHE B 400 
 TRP   0.009   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6676)
  covalent geometry    : angle       0.57213 ( 9076)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       1.39075 (    8)
  hydrogen bonds       : bond        0.05345 (  292)
  hydrogen bonds       : angle       4.05223 (  818)
  metal coordination   : bond        0.00197 (    2)
  link_NAG-ASN         : bond        0.00647 (    6)
  link_NAG-ASN         : angle       3.22944 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7576 (ptm160)
REVERT: A  440 LYS cc_start: 0.8763 (mttm) cc_final: 0.8418 (mmtm)
REVERT: B  341 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7167 (mmmt)
  outliers start: 15
  outliers final: 11
  residues processed: 83
  average time/residue: 0.5980
  time to fit residues: 52.3617
Evaluate side-chains
  82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 HIS
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.154428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.111711 restraints weight = 15500.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.86
r_work: 0.3095 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6688  Z= 0.131
  Angle     :  0.584  10.265   9102  Z= 0.289
  Chirality :  0.043   0.389    964
  Planarity :  0.004   0.047   1170
  Dihedral  :  5.408  55.084    985
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.95 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.01 %
    Favored  : 83.12 %
  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 aren not related in a simple way.
  whole:  0.66 (0.30), residues: 785
  helix:  1.67 (0.28), residues: 364
  sheet:  0.79 (0.67), residues: 55
  loop : -0.91 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 501 
 PHE   0.015   0.001   PHE B 400 
 TRP   0.009   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6676)
  covalent geometry    : angle       0.56620 ( 9076)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       1.42419 (    8)
  hydrogen bonds       : bond        0.05169 (  292)
  hydrogen bonds       : angle       3.98893 (  818)
  metal coordination   : bond        0.00148 (    2)
  link_NAG-ASN         : bond        0.00633 (    6)
  link_NAG-ASN         : angle       3.15169 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7363 (ptm160)
REVERT: A  440 LYS cc_start: 0.8744 (mttm) cc_final: 0.8400 (mmtm)
REVERT: B  102 GLN cc_start: 0.7951 (pt0) cc_final: 0.7283 (mm110)
REVERT: B  341 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7110 (mmmt)
REVERT: B  376 MET cc_start: 0.8696 (ttm) cc_final: 0.8473 (ttt)
  outliers start: 13
  outliers final: 11
  residues processed: 88
  average time/residue: 0.5763
  time to fit residues: 53.4002
Evaluate side-chains
  84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0980
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 HIS
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.155494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.118956 restraints weight = 7688.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.91
r_work: 0.3181 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6688  Z= 0.144
  Angle     :  0.596  10.243   9102  Z= 0.297
  Chirality :  0.044   0.390    964
  Planarity :  0.004   0.047   1170
  Dihedral  :  5.414  55.616    985
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.34 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.15 %
    Favored  : 82.97 %
  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 aren not related in a simple way.
  whole:  0.63 (0.30), residues: 785
  helix:  1.64 (0.28), residues: 364
  sheet:  0.75 (0.67), residues: 55
  loop : -0.91 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 357 
 TYR   0.017   0.001   TYR A 501 
 PHE   0.018   0.001   PHE B 400 
 TRP   0.008   0.001   TRP B 477 
 HIS   0.010   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6676)
  covalent geometry    : angle       0.57888 ( 9076)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       1.56643 (    8)
  hydrogen bonds       : bond        0.05515 (  292)
  hydrogen bonds       : angle       4.03348 (  818)
  metal coordination   : bond        0.00183 (    2)
  link_NAG-ASN         : bond        0.00623 (    6)
  link_NAG-ASN         : angle       3.09954 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7504 (ptm160)
REVERT: A  440 LYS cc_start: 0.8781 (mttm) cc_final: 0.8453 (mmtm)
REVERT: B  102 GLN cc_start: 0.8108 (pt0) cc_final: 0.7481 (mm110)
REVERT: B  341 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7173 (mmmt)
  outliers start: 13
  outliers final: 11
  residues processed: 81
  average time/residue: 0.6080
  time to fit residues: 51.9288
Evaluate side-chains
  81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   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 334 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 HIS
B 472 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.156188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122822 restraints weight = 15476.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 4.10
r_work: 0.3098 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6688  Z= 0.137
  Angle     :  0.590  10.267   9102  Z= 0.293
  Chirality :  0.043   0.389    964
  Planarity :  0.004   0.047   1170
  Dihedral  :  5.327  55.299    985
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.95 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.58 %
    Favored  : 82.68 %
  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 aren not related in a simple way.
  whole:  0.64 (0.30), residues: 785
  helix:  1.64 (0.27), residues: 364
  sheet:  0.73 (0.67), residues: 55
  loop : -0.89 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 501 
 PHE   0.015   0.001   PHE B 400 
 TRP   0.009   0.001   TRP B 477 
 HIS   0.011   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6676)
  covalent geometry    : angle       0.57355 ( 9076)
  SS BOND              : bond        0.00257 (    4)
  SS BOND              : angle       1.56184 (    8)
  hydrogen bonds       : bond        0.05308 (  292)
  hydrogen bonds       : angle       4.03517 (  818)
  metal coordination   : bond        0.00169 (    2)
  link_NAG-ASN         : bond        0.00634 (    6)
  link_NAG-ASN         : angle       3.03263 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7493 (ptm160)
REVERT: A  440 LYS cc_start: 0.8738 (mttm) cc_final: 0.8417 (mmtm)
REVERT: B  102 GLN cc_start: 0.8036 (pt0) cc_final: 0.7393 (mm110)
REVERT: B  341 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7098 (mmmt)
  outliers start: 12
  outliers final: 11
  residues processed: 78
  average time/residue: 0.5987
  time to fit residues: 49.1711
Evaluate side-chains
  81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 HIS
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.155357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.120956 restraints weight = 11702.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.98
r_work: 0.3120 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6688  Z= 0.143
  Angle     :  0.594  10.223   9102  Z= 0.297
  Chirality :  0.044   0.390    964
  Planarity :  0.004   0.047   1170
  Dihedral  :  5.344  55.586    985
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.21 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.73 %
    Favored  : 82.54 %
  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 aren not related in a simple way.
  whole:  0.66 (0.30), residues: 785
  helix:  1.65 (0.27), residues: 364
  sheet:  0.77 (0.67), residues: 55
  loop : -0.88 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.017   0.001   TYR A 501 
 PHE   0.017   0.001   PHE B 400 
 TRP   0.008   0.001   TRP B 477 
 HIS   0.013   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6676)
  covalent geometry    : angle       0.57804 ( 9076)
  SS BOND              : bond        0.00262 (    4)
  SS BOND              : angle       1.57330 (    8)
  hydrogen bonds       : bond        0.05493 (  292)
  hydrogen bonds       : angle       4.04457 (  818)
  metal coordination   : bond        0.00189 (    2)
  link_NAG-ASN         : bond        0.00619 (    6)
  link_NAG-ASN         : angle       3.01693 (   18)

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

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7612 (ptm160)
REVERT: A  440 LYS cc_start: 0.8797 (mttm) cc_final: 0.8440 (mmtm)
REVERT: B  102 GLN cc_start: 0.8087 (pt0) cc_final: 0.7423 (mm110)
REVERT: B  341 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7147 (mmmt)
REVERT: B  376 MET cc_start: 0.8803 (ttm) cc_final: 0.8592 (ttt)
  outliers start: 12
  outliers final: 11
  residues processed: 78
  average time/residue: 0.6019
  time to fit residues: 49.5682
Evaluate side-chains
  82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  530 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 HIS
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.155333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.118837 restraints weight = 7660.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.92
r_work: 0.3181 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6688  Z= 0.143
  Angle     :  0.596  10.212   9102  Z= 0.298
  Chirality :  0.044   0.390    964
  Planarity :  0.004   0.047   1170
  Dihedral  :  5.351  55.578    985
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.95 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.44 %
    Favored  : 82.54 %
  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 aren not related in a simple way.
  whole:  0.68 (0.30), residues: 785
  helix:  1.67 (0.27), residues: 364
  sheet:  0.76 (0.67), residues: 55
  loop : -0.86 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.017   0.001   TYR A 501 
 PHE   0.017   0.001   PHE B 400 
 TRP   0.008   0.001   TRP B 477 
 HIS   0.015   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6676)
  covalent geometry    : angle       0.58055 ( 9076)
  SS BOND              : bond        0.00254 (    4)
  SS BOND              : angle       1.54373 (    8)
  hydrogen bonds       : bond        0.05497 (  292)
  hydrogen bonds       : angle       4.02608 (  818)
  metal coordination   : bond        0.00191 (    2)
  link_NAG-ASN         : bond        0.00620 (    6)
  link_NAG-ASN         : angle       2.98439 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2832.24 seconds
wall clock time: 49 minutes 1.34 seconds (2941.34 seconds total)