Starting phenix.real_space_refine
on Sat Oct 11 01:29:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y18_38827/10_2025/8y18_38827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y18_38827/10_2025/8y18_38827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y18_38827/10_2025/8y18_38827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y18_38827/10_2025/8y18_38827.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y18_38827/10_2025/8y18_38827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y18_38827/10_2025/8y18_38827.map"
  }
  resolution = 3.04
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4869 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      36      5.16       5
     C    4198      2.51       5
     N    1070      2.21       5
     O    1260      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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6565
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    Chain: "B"
      Number of atoms: 1491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1491
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 11, 'TRANS': 172}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' ZN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.06, per 1000 atoms: 0.47
  Number of scatterers: 6565
  At special positions: 0
  Unit cell: (92.46, 76.59, 112.47, 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      36     16.00
     O    1260      8.00
     N    1070      7.00
     C    4198      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A 702 " - " ASN A  53 "
      " NAG A 703 " - " ASN A 432 "
      " NAG B1301 " - " ASN B 354 "
      " NAG C   1 " - " ASN A  90 "
      " NAG D   1 " - " ASN A 322 "
      " NAG E   1 " - " ASN A 546 "
      " NAG F   1 " - " ASN A 103 "
      " NAG G   1 " - " ASN B 343 "
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 550.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "


  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1474

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 6 sheets defined
      55.6% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 4.068A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 79
      removed outlier: 3.536A  pdb=" N   THR A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 83
      removed outlier: 3.836A  pdb=" N   TYR A  83 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 80 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.917A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 92 through 101
      removed outlier: 3.951A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 147 through 154
    Processing helix  chain 'A' and resid 158 through 194
      removed outlier: 3.740A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 248
      removed outlier: 4.092A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ILE A 233 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LYS A 234 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 249 through 251
      No H-bonds generated for 'chain 'A' and resid 249 through 251'
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.581A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.754A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.627A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 4.241A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.796A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.734A  pdb=" N   THR A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.562A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.766A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 581 through 587
      removed outlier: 3.531A  pdb=" N   LEU A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 372
      removed outlier: 3.761A  pdb=" N   TYR B 369 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 390
      removed outlier: 3.819A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 439 through 442
      removed outlier: 3.546A  pdb=" N   ASP B 442 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 439 through 442'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.467A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.111A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.564A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 379
      removed outlier: 4.024A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA B 435 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE B 434 " --> pdb=" O   VAL B 511 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453

    269 hydrogen bonds defined for protein.
    758 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: 1.03

  Time building geometry restraints manager: 0.83 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: 2066
        1.34 -     1.46: 1659
        1.46 -     1.58: 2970
        1.58 -     1.70: 1
        1.70 -     1.81: 57
  Bond restraints: 6753
  Sorted by residual:
  bond pdb=" N   ASN B 354 "
       pdb=" CA  ASN B 354 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.031 1.34e-02 5.57e+03 5.22e+00
  bond pdb=" N   ASN A 322 "
       pdb=" CA  ASN A 322 "
    ideal  model  delta    sigma   weight residual
    1.455  1.478 -0.022 1.09e-02 8.42e+03 4.19e+00
  bond pdb=" CA  GLN A  89 "
       pdb=" CB  GLN A  89 "
    ideal  model  delta    sigma   weight residual
    1.531  1.592 -0.062 3.12e-02 1.03e+03 3.90e+00
  bond pdb=" N   ALA B 344 "
       pdb=" CA  ALA B 344 "
    ideal  model  delta    sigma   weight residual
    1.456  1.478 -0.022 1.14e-02 7.69e+03 3.66e+00
  bond pdb=" C2  BMA D   3 "
       pdb=" C3  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.544  1.507  0.037 2.00e-02 2.50e+03 3.39e+00
  ... (remaining 6748 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 8803
        1.39 -     2.78: 268
        2.78 -     4.18: 81
        4.18 -     5.57: 22
        5.57 -     6.96: 3
  Bond angle restraints: 9177
  Sorted by residual:
  angle pdb=" N   PHE B 342 "
        pdb=" CA  PHE B 342 "
        pdb=" C   PHE B 342 "
      ideal   model   delta    sigma   weight residual
     112.88  107.82    5.06 1.29e+00 6.01e-01 1.54e+01
  angle pdb=" O   ALA B 352 "
        pdb=" C   ALA B 352 "
        pdb=" N   TRP B 353 "
      ideal   model   delta    sigma   weight residual
     122.59  127.13   -4.54 1.33e+00 5.65e-01 1.17e+01
  angle pdb=" C   PRO A 321 "
        pdb=" N   ASN A 322 "
        pdb=" CA  ASN A 322 "
      ideal   model   delta    sigma   weight residual
     122.15  116.47    5.68 1.74e+00 3.30e-01 1.07e+01
  angle pdb=" CA  ASN B 343 "
        pdb=" C   ASN B 343 "
        pdb=" O   ASN B 343 "
      ideal   model   delta    sigma   weight residual
     121.67  118.85    2.82 9.30e-01 1.16e+00 9.19e+00
  angle pdb=" C   ASN A 322 "
        pdb=" CA  ASN A 322 "
        pdb=" CB  ASN A 322 "
      ideal   model   delta    sigma   weight residual
     114.16  107.20    6.96 2.31e+00 1.87e-01 9.08e+00
  ... (remaining 9172 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.23: 3853
       21.23 -    42.46: 250
       42.46 -    63.70: 35
       63.70 -    84.93: 21
       84.93 -   106.16: 10
  Dihedral angle restraints: 4169
    sinusoidal: 1872
      harmonic: 2297
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.96   81.96     1      1.00e+01 1.00e-02 8.26e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.53  -68.47     1      1.00e+01 1.00e-02 6.08e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.68   31.68     1      1.00e+01 1.00e-02 1.43e+01
  ... (remaining 4166 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.166: 980
       0.166 -    0.332: 12
       0.332 -    0.499: 0
       0.499 -    0.665: 2
       0.665 -    0.831: 1
  Chirality restraints: 995
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.78   -0.62 2.00e-02 2.50e+03 9.71e+02
  chirality pdb=" C1  BMA D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.83   -0.57 2.00e-02 2.50e+03 8.08e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-02 2.50e+03 1.71e+02
  ... (remaining 992 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   2 "    0.298 2.00e-02 2.50e+03   2.57e-01 8.26e+02
        pdb=" C7  NAG G   2 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8  NAG G   2 "    0.155 2.00e-02 2.50e+03
        pdb=" N2  NAG G   2 "   -0.456 2.00e-02 2.50e+03
        pdb=" O7  NAG G   2 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   1 "   -0.233 2.00e-02 2.50e+03   1.96e-01 4.82e+02
        pdb=" C7  NAG G   1 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG G   1 "   -0.160 2.00e-02 2.50e+03
        pdb=" N2  NAG G   1 "    0.329 2.00e-02 2.50e+03
        pdb=" O7  NAG G   1 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1301 "   -0.157 2.00e-02 2.50e+03   1.32e-01 2.17e+02
        pdb=" C7  NAG B1301 "    0.042 2.00e-02 2.50e+03
        pdb=" C8  NAG B1301 "   -0.114 2.00e-02 2.50e+03
        pdb=" N2  NAG B1301 "    0.217 2.00e-02 2.50e+03
        pdb=" O7  NAG B1301 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 79
        2.66 -     3.22: 5992
        3.22 -     3.78: 9533
        3.78 -     4.34: 12683
        4.34 -     4.90: 20686
  Nonbonded interactions: 48973
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.100 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.108 2.230
  nonbonded pdb=" NE2 HIS A 374 "
            pdb=" OE1 GLU A 402 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" NE2 GLN B 474 "
            pdb=" O   GLY B 476 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OD1 ASN A 134 "
            pdb=" ND2 ASN A 137 "
     model   vdw
     2.275 3.120
  ... (remaining 48968 not shown)

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

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=0.37 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:             16.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.440
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6503
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      :  0.005   0.207   6776  Z= 0.233
  Angle     :  0.828  17.801   9234  Z= 0.384
  Chirality :  0.063   0.831    995
  Planarity :  0.013   0.257   1166
  Dihedral  : 15.606 106.161   2677
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.26 (0.31), residues: 777
  helix:  1.82 (0.29), residues: 344
  sheet: -1.32 (0.88), residues: 26
  loop : -1.23 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.012   0.001   TYR A 385 
 PHE   0.012   0.001   PHE B 338 
 TRP   0.019   0.002   TRP A 203 
 HIS   0.012   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6753)
  covalent geometry    : angle       0.65084 ( 9177)
  SS BOND              : bond        0.00196 (    6)
  SS BOND              : angle       0.64217 (   12)
  hydrogen bonds       : bond        0.16932 (  269)
  hydrogen bonds       : angle       5.28247 (  758)
  metal coordination   : bond        0.20497 (    2)
  link_BETA1-4         : bond        0.04597 (    7)
  link_BETA1-4         : angle       8.35650 (   21)
  link_NAG-ASN         : bond        0.01470 (    8)
  link_NAG-ASN         : angle       6.35494 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 THR cc_start: 0.8241 (p) cc_final: 0.7924 (p)
REVERT: B  492 LEU cc_start: 0.7615 (mt) cc_final: 0.7133 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0947
  time to fit residues: 15.7229
Evaluate side-chains
  63 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS    B
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.062178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.050076 restraints weight = 48467.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 5.73
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3456
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6776  Z= 0.159
  Angle     :  0.729   9.248   9234  Z= 0.357
  Chirality :  0.046   0.373    995
  Planarity :  0.004   0.035   1166
  Dihedral  :  9.884  67.491   1160
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.90 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.12 (0.31), residues: 777
  helix:  1.51 (0.28), residues: 358
  sheet: -1.17 (0.95), residues: 31
  loop : -1.23 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 582 
 TYR   0.020   0.002   TYR A  50 
 PHE   0.015   0.001   PHE B 515 
 TRP   0.020   0.001   TRP A 606 
 HIS   0.005   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6753)
  covalent geometry    : angle       0.69111 ( 9177)
  SS BOND              : bond        0.00274 (    6)
  SS BOND              : angle       0.64072 (   12)
  hydrogen bonds       : bond        0.05310 (  269)
  hydrogen bonds       : angle       4.55170 (  758)
  metal coordination   : bond        0.00576 (    2)
  link_BETA1-4         : bond        0.01440 (    7)
  link_BETA1-4         : angle       3.15909 (   21)
  link_NAG-ASN         : bond        0.00414 (    8)
  link_NAG-ASN         : angle       3.55896 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 67
  average time/residue: 0.0823
  time to fit residues: 7.6174
Evaluate side-chains
  51 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  444 LYS
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 16 optimal weight:    0.2980
   chunk 8 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.061069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.048582 restraints weight = 60097.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 6.42
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6776  Z= 0.129
  Angle     :  0.647   9.719   9234  Z= 0.314
  Chirality :  0.044   0.326    995
  Planarity :  0.004   0.030   1166
  Dihedral  :  7.614  59.025   1160
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.48 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.20 (0.31), residues: 777
  helix:  1.61 (0.29), residues: 355
  sheet: -1.11 (0.93), residues: 31
  loop : -1.21 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 582 
 TYR   0.012   0.001   TYR A 158 
 PHE   0.012   0.001   PHE B 490 
 TRP   0.016   0.001   TRP A 610 
 HIS   0.004   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6753)
  covalent geometry    : angle       0.61344 ( 9177)
  SS BOND              : bond        0.00205 (    6)
  SS BOND              : angle       0.73772 (   12)
  hydrogen bonds       : bond        0.04586 (  269)
  hydrogen bonds       : angle       4.23431 (  758)
  metal coordination   : bond        0.00058 (    2)
  link_BETA1-4         : bond        0.01229 (    7)
  link_BETA1-4         : angle       3.03417 (   21)
  link_NAG-ASN         : bond        0.00314 (    8)
  link_NAG-ASN         : angle       2.95356 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 MET cc_start: 0.9051 (tpp) cc_final: 0.8720 (tpp)
REVERT: A  455 MET cc_start: 0.8340 (tmm) cc_final: 0.7898 (tmm)
  outliers start: 6
  outliers final: 4
  residues processed: 58
  average time/residue: 0.0706
  time to fit residues: 5.9943
Evaluate side-chains
  50 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 52 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 401 HIS
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.059486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.046572 restraints weight = 73176.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 6.95
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6776  Z= 0.146
  Angle     :  0.638   8.400   9234  Z= 0.312
  Chirality :  0.044   0.315    995
  Planarity :  0.004   0.030   1166
  Dihedral  :  6.548  55.633   1160
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.52 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.30 (0.31), residues: 777
  helix:  1.64 (0.28), residues: 356
  sheet: -1.20 (0.90), residues: 31
  loop : -1.08 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 245 
 TYR   0.011   0.001   TYR A 158 
 PHE   0.015   0.001   PHE A 230 
 TRP   0.012   0.001   TRP A 610 
 HIS   0.006   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6753)
  covalent geometry    : angle       0.60716 ( 9177)
  SS BOND              : bond        0.00512 (    6)
  SS BOND              : angle       1.14613 (   12)
  hydrogen bonds       : bond        0.04537 (  269)
  hydrogen bonds       : angle       4.24753 (  758)
  metal coordination   : bond        0.00242 (    2)
  link_BETA1-4         : bond        0.01252 (    7)
  link_BETA1-4         : angle       2.82831 (   21)
  link_NAG-ASN         : bond        0.00287 (    8)
  link_NAG-ASN         : angle       2.86534 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8870 (tp30) cc_final: 0.8475 (tm-30)
REVERT: A  270 MET cc_start: 0.8625 (tpt) cc_final: 0.8376 (tpt)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0721
  time to fit residues: 5.3715
Evaluate side-chains
  50 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0570
   overall best weight:    0.5702

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

Flipped N/Q/H residues before XYZ refinement:
A 524 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.059924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.047410 restraints weight = 59422.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 6.27
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6776  Z= 0.107
  Angle     :  0.600   8.383   9234  Z= 0.287
  Chirality :  0.043   0.310    995
  Planarity :  0.003   0.029   1166
  Dihedral  :  6.024  53.832   1160
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.95 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.33 (0.31), residues: 777
  helix:  1.68 (0.28), residues: 354
  sheet: -1.16 (0.84), residues: 31
  loop : -1.06 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 582 
 TYR   0.013   0.001   TYR A 158 
 PHE   0.008   0.001   PHE A 525 
 TRP   0.010   0.001   TRP A 610 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6753)
  covalent geometry    : angle       0.57025 ( 9177)
  SS BOND              : bond        0.00073 (    6)
  SS BOND              : angle       1.24999 (   12)
  hydrogen bonds       : bond        0.03981 (  269)
  hydrogen bonds       : angle       4.09553 (  758)
  metal coordination   : bond        0.00140 (    2)
  link_BETA1-4         : bond        0.01248 (    7)
  link_BETA1-4         : angle       2.63082 (   21)
  link_NAG-ASN         : bond        0.00359 (    8)
  link_NAG-ASN         : angle       2.68675 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8909 (tp30) cc_final: 0.8577 (tm-30)
REVERT: A  475 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8734 (mmtm)
  outliers start: 6
  outliers final: 4
  residues processed: 55
  average time/residue: 0.0717
  time to fit residues: 5.7213
Evaluate side-chains
  46 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0270
   chunk 4 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.059364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.046763 restraints weight = 73980.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 6.91
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3365
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3365
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6776  Z= 0.111
  Angle     :  0.628  12.492   9234  Z= 0.300
  Chirality :  0.043   0.304    995
  Planarity :  0.003   0.027   1166
  Dihedral  :  6.029  54.342   1160
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 14.12 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.37 (0.31), residues: 777
  helix:  1.70 (0.29), residues: 355
  sheet: -1.22 (0.70), residues: 43
  loop : -1.02 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A  50 
 PHE   0.020   0.001   PHE B 456 
 TRP   0.010   0.001   TRP A 610 
 HIS   0.011   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6753)
  covalent geometry    : angle       0.59965 ( 9177)
  SS BOND              : bond        0.00519 (    6)
  SS BOND              : angle       1.70724 (   12)
  hydrogen bonds       : bond        0.03974 (  269)
  hydrogen bonds       : angle       4.03405 (  758)
  metal coordination   : bond        0.00121 (    2)
  link_BETA1-4         : bond        0.01221 (    7)
  link_BETA1-4         : angle       2.52432 (   21)
  link_NAG-ASN         : bond        0.00295 (    8)
  link_NAG-ASN         : angle       2.66413 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8920 (tp30) cc_final: 0.8632 (tm-30)
  outliers start: 8
  outliers final: 5
  residues processed: 48
  average time/residue: 0.0667
  time to fit residues: 4.8135
Evaluate side-chains
  44 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0470
   chunk 25 optimal weight:    0.0970
   chunk 14 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 44 optimal weight:    0.2980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.059881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.047900 restraints weight = 49789.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 5.60
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6776  Z= 0.105
  Angle     :  0.613   9.392   9234  Z= 0.292
  Chirality :  0.042   0.302    995
  Planarity :  0.003   0.027   1166
  Dihedral  :  5.940  54.316   1160
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.68 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.42 (0.31), residues: 777
  helix:  1.65 (0.29), residues: 363
  sheet: -1.03 (0.86), residues: 31
  loop : -0.98 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A 158 
 PHE   0.014   0.001   PHE B 456 
 TRP   0.009   0.001   TRP A 610 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6753)
  covalent geometry    : angle       0.58494 ( 9177)
  SS BOND              : bond        0.00331 (    6)
  SS BOND              : angle       1.78761 (   12)
  hydrogen bonds       : bond        0.03776 (  269)
  hydrogen bonds       : angle       3.98168 (  758)
  metal coordination   : bond        0.00074 (    2)
  link_BETA1-4         : bond        0.01164 (    7)
  link_BETA1-4         : angle       2.45413 (   21)
  link_NAG-ASN         : bond        0.00336 (    8)
  link_NAG-ASN         : angle       2.59211 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8936 (tp30) cc_final: 0.8651 (tm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 48
  average time/residue: 0.0659
  time to fit residues: 4.7654
Evaluate side-chains
  44 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0770
   chunk 21 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0770
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.059565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.046709 restraints weight = 79393.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 7.14
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6776  Z= 0.105
  Angle     :  0.608  10.112   9234  Z= 0.289
  Chirality :  0.042   0.292    995
  Planarity :  0.003   0.027   1166
  Dihedral  :  5.925  54.579   1160
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 13.97 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.58 (0.32), residues: 777
  helix:  1.74 (0.29), residues: 362
  sheet: -0.95 (0.87), residues: 31
  loop : -0.84 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 357 
 TYR   0.010   0.001   TYR A 158 
 PHE   0.012   0.001   PHE B 456 
 TRP   0.010   0.001   TRP A 610 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6753)
  covalent geometry    : angle       0.58190 ( 9177)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       1.80295 (   12)
  hydrogen bonds       : bond        0.03674 (  269)
  hydrogen bonds       : angle       3.95994 (  758)
  metal coordination   : bond        0.00107 (    2)
  link_BETA1-4         : bond        0.01094 (    7)
  link_BETA1-4         : angle       2.33583 (   21)
  link_NAG-ASN         : bond        0.00287 (    8)
  link_NAG-ASN         : angle       2.56641 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7692 (ptm) cc_final: 0.6975 (ppp)
REVERT: A  189 GLU cc_start: 0.8995 (tp30) cc_final: 0.8750 (tm-30)
REVERT: A  360 MET cc_start: 0.8132 (mmp) cc_final: 0.7659 (mmm)
  outliers start: 6
  outliers final: 5
  residues processed: 46
  average time/residue: 0.0632
  time to fit residues: 4.4528
Evaluate side-chains
  42 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 39 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0770
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.059548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.047619 restraints weight = 49989.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 5.51
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6776  Z= 0.102
  Angle     :  0.599   8.640   9234  Z= 0.284
  Chirality :  0.042   0.297    995
  Planarity :  0.003   0.027   1166
  Dihedral  :  5.901  54.500   1160
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 14.12 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 (0.32), residues: 777
  helix:  1.75 (0.29), residues: 364
  sheet: -0.83 (0.72), residues: 41
  loop : -0.75 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 559 
 TYR   0.009   0.001   TYR A 158 
 PHE   0.010   0.001   PHE B 456 
 TRP   0.009   0.001   TRP A 610 
 HIS   0.004   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6753)
  covalent geometry    : angle       0.57412 ( 9177)
  SS BOND              : bond        0.00327 (    6)
  SS BOND              : angle       1.53050 (   12)
  hydrogen bonds       : bond        0.03613 (  269)
  hydrogen bonds       : angle       3.94367 (  758)
  metal coordination   : bond        0.00098 (    2)
  link_BETA1-4         : bond        0.01067 (    7)
  link_BETA1-4         : angle       2.26923 (   21)
  link_NAG-ASN         : bond        0.00322 (    8)
  link_NAG-ASN         : angle       2.54785 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8939 (tp30) cc_final: 0.8716 (tm-30)
REVERT: A  360 MET cc_start: 0.8045 (mmp) cc_final: 0.7427 (mmp)
  outliers start: 7
  outliers final: 6
  residues processed: 46
  average time/residue: 0.0649
  time to fit residues: 4.6894
Evaluate side-chains
  43 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.059106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.046794 restraints weight = 59950.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 6.14
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6776  Z= 0.109
  Angle     :  0.609   8.497   9234  Z= 0.291
  Chirality :  0.042   0.289    995
  Planarity :  0.003   0.027   1166
  Dihedral  :  5.956  54.608   1160
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.26 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 (0.32), residues: 777
  helix:  1.69 (0.29), residues: 363
  sheet: -0.84 (0.71), residues: 43
  loop : -0.69 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.010   0.001   TYR A 158 
 PHE   0.009   0.001   PHE B 456 
 TRP   0.010   0.001   TRP A 610 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6753)
  covalent geometry    : angle       0.58504 ( 9177)
  SS BOND              : bond        0.00297 (    6)
  SS BOND              : angle       1.58701 (   12)
  hydrogen bonds       : bond        0.03700 (  269)
  hydrogen bonds       : angle       4.04156 (  758)
  metal coordination   : bond        0.00423 (    2)
  link_BETA1-4         : bond        0.01005 (    7)
  link_BETA1-4         : angle       2.18513 (   21)
  link_NAG-ASN         : bond        0.00277 (    8)
  link_NAG-ASN         : angle       2.53863 (   24)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7764 (ptm) cc_final: 0.7149 (ppp)
REVERT: A  189 GLU cc_start: 0.8975 (tp30) cc_final: 0.8742 (tm-30)
REVERT: A  360 MET cc_start: 0.7995 (mmp) cc_final: 0.7452 (mmp)
  outliers start: 6
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0760
  time to fit residues: 4.8912
Evaluate side-chains
  43 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  517 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0870
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.059023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.046220 restraints weight = 79737.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 7.10
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.4848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6776  Z= 0.107
  Angle     :  0.634  14.389   9234  Z= 0.302
  Chirality :  0.042   0.296    995
  Planarity :  0.003   0.027   1166
  Dihedral  :  5.966  54.509   1160
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 13.83 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.32), residues: 777
  helix:  1.67 (0.29), residues: 364
  sheet: -0.81 (0.71), residues: 43
  loop : -0.71 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.010   0.001   TYR A 158 
 PHE   0.009   0.001   PHE B 456 
 TRP   0.010   0.001   TRP A 610 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6753)
  covalent geometry    : angle       0.61162 ( 9177)
  SS BOND              : bond        0.00267 (    6)
  SS BOND              : angle       1.56050 (   12)
  hydrogen bonds       : bond        0.03717 (  269)
  hydrogen bonds       : angle       4.12040 (  758)
  metal coordination   : bond        0.00120 (    2)
  link_BETA1-4         : bond        0.00981 (    7)
  link_BETA1-4         : angle       2.12251 (   21)
  link_NAG-ASN         : bond        0.00321 (    8)
  link_NAG-ASN         : angle       2.54230 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2209.67 seconds
wall clock time: 38 minutes 37.02 seconds (2317.02 seconds total)