Starting phenix.real_space_refine
on Mon Jul 28 17:04:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y18_38827/07_2025/8y18_38827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y18_38827/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y18_38827/07_2025/8y18_38827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y18_38827/07_2025/8y18_38827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y18_38827/07_2025/8y18_38827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y18_38827/07_2025/8y18_38827.cif"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.04, per 1000 atoms: 1.68
  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: 2.21
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  
  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: 0.80
  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: 2.27

  Time building geometry restraints manager: 2.28 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:             867.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     29.570
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:3.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  900.690
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (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
 TRP   0.019   0.002   TRP A 203 
 HIS   0.012   0.001   HIS A 401 
 PHE   0.012   0.001   PHE B 338 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.002   0.000   ARG B 457 

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

*********************** 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  : 1.227 
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: 0.3054
  time to fit residues: 50.1373
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  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    8.9990
   overall best weight:    0.9362

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.062254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.049325 restraints weight = 71454.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 7.11
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6776  Z= 0.159
  Angle     :  0.725   9.125   9234  Z= 0.354
  Chirality :  0.046   0.370    995
  Planarity :  0.004   0.033   1166
  Dihedral  :  9.899  68.040   1160
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.04 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.31), residues: 777
  helix:  1.52 (0.28), residues: 358
  sheet: -1.17 (0.95), residues: 31
  loop : -1.25 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 606 
 HIS   0.006   0.001   HIS A 378 
 PHE   0.016   0.001   PHE B 515 
 TYR   0.019   0.002   TYR A  50 
 ARG   0.008   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    8)
  link_NAG-ASN         : angle       3.56668 (   24)
  link_BETA1-4         : bond        0.01269 (    7)
  link_BETA1-4         : angle       3.22650 (   21)
  hydrogen bonds       : bond        0.05332 (  269)
  hydrogen bonds       : angle       4.54694 (  758)
  metal coordination   : bond        0.00941 (    2)
  SS BOND              : bond        0.00281 (    6)
  SS BOND              : angle       0.66096 (   12)
  covalent geometry    : bond        0.00356 ( 6753)
  covalent geometry    : angle       0.68634 ( 9177)

*********************** 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  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 67
  average time/residue: 0.2231
  time to fit residues: 20.1745
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  : 0.712 
-------------------------------------------------------------------------------
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 8 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 101 GLN
A 401 HIS
A 508 ASN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.058138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.045835 restraints weight = 50436.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 5.66
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6776  Z= 0.228
  Angle     :  0.741   8.955   9234  Z= 0.367
  Chirality :  0.046   0.331    995
  Planarity :  0.005   0.036   1166
  Dihedral  :  7.683  59.082   1160
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.21 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.31), residues: 777
  helix:  1.33 (0.28), residues: 359
  sheet: -1.72 (0.83), residues: 36
  loop : -1.19 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 610 
 HIS   0.008   0.002   HIS A 378 
 PHE   0.024   0.002   PHE A 230 
 TYR   0.017   0.002   TYR A 515 
 ARG   0.006   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00484 (    8)
  link_NAG-ASN         : angle       3.08650 (   24)
  link_BETA1-4         : bond        0.01131 (    7)
  link_BETA1-4         : angle       3.01492 (   21)
  hydrogen bonds       : bond        0.05408 (  269)
  hydrogen bonds       : angle       4.49208 (  758)
  metal coordination   : bond        0.00447 (    2)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       0.98219 (   12)
  covalent geometry    : bond        0.00507 ( 6753)
  covalent geometry    : angle       0.71146 ( 9177)

*********************** 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
  57 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: A  455 MET cc_start: 0.8332 (tmm) cc_final: 0.7970 (tmm)
  outliers start: 11
  outliers final: 6
  residues processed: 54
  average time/residue: 0.1945
  time to fit residues: 14.6297
Evaluate side-chains
  49 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  468 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0970
   chunk 37 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.058801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.046576 restraints weight = 52406.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 5.76
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    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 = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6776  Z= 0.123
  Angle     :  0.651   9.292   9234  Z= 0.314
  Chirality :  0.043   0.332    995
  Planarity :  0.004   0.031   1166
  Dihedral  :  6.646  55.268   1160
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.79 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.31), residues: 777
  helix:  1.60 (0.28), residues: 356
  sheet: -1.12 (0.88), residues: 31
  loop : -1.12 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 606 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.018   0.001   PHE B 456 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.003   0.000   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00322 (    8)
  link_NAG-ASN         : angle       2.95678 (   24)
  link_BETA1-4         : bond        0.01172 (    7)
  link_BETA1-4         : angle       2.79807 (   21)
  hydrogen bonds       : bond        0.04554 (  269)
  hydrogen bonds       : angle       4.33824 (  758)
  metal coordination   : bond        0.00187 (    2)
  SS BOND              : bond        0.00237 (    6)
  SS BOND              : angle       2.89536 (   12)
  covalent geometry    : bond        0.00269 ( 6753)
  covalent geometry    : angle       0.61204 ( 9177)

*********************** 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
  55 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8849 (tp30) cc_final: 0.8446 (tm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 54
  average time/residue: 0.1855
  time to fit residues: 15.2921
Evaluate side-chains
  48 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain B residue  477 ASN
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 70 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 25 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0770
   chunk 38 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.6744

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.057287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.045455 restraints weight = 41295.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 4.97
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6776  Z= 0.173
  Angle     :  0.660   8.210   9234  Z= 0.322
  Chirality :  0.044   0.326    995
  Planarity :  0.004   0.032   1166
  Dihedral  :  6.489  54.560   1160
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.37 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.31), residues: 777
  helix:  1.33 (0.28), residues: 368
  sheet: -1.62 (0.80), residues: 36
  loop : -1.12 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 610 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.015   0.001   PHE A 230 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.003   0.000   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00342 (    8)
  link_NAG-ASN         : angle       2.92955 (   24)
  link_BETA1-4         : bond        0.01189 (    7)
  link_BETA1-4         : angle       2.63766 (   21)
  hydrogen bonds       : bond        0.04764 (  269)
  hydrogen bonds       : angle       4.34785 (  758)
  metal coordination   : bond        0.00401 (    2)
  SS BOND              : bond        0.00155 (    6)
  SS BOND              : angle       2.77698 (   12)
  covalent geometry    : bond        0.00386 ( 6753)
  covalent geometry    : angle       0.62491 ( 9177)

*********************** 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
  53 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9217 (mmt) cc_final: 0.8918 (mmp)
REVERT: A  189 GLU cc_start: 0.8904 (tp30) cc_final: 0.8570 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 52
  average time/residue: 0.1971
  time to fit residues: 14.8493
Evaluate side-chains
  43 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  477 ASN
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 52 optimal weight:    0.0470
   chunk 27 optimal weight:    0.0770
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.4636

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.058351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.045419 restraints weight = 79507.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 7.16
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4587

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= 0.107
  Angle     :  0.610   8.133   9234  Z= 0.292
  Chirality :  0.042   0.330    995
  Planarity :  0.003   0.030   1166
  Dihedral  :  6.139  54.080   1160
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 13.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.31), residues: 777
  helix:  1.49 (0.28), residues: 364
  sheet: -0.88 (0.87), residues: 31
  loop : -1.10 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 606 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 315 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.002   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00389 (    8)
  link_NAG-ASN         : angle       2.85884 (   24)
  link_BETA1-4         : bond        0.01201 (    7)
  link_BETA1-4         : angle       2.53487 (   21)
  hydrogen bonds       : bond        0.04085 (  269)
  hydrogen bonds       : angle       4.15321 (  758)
  metal coordination   : bond        0.00102 (    2)
  SS BOND              : bond        0.00107 (    6)
  SS BOND              : angle       2.08472 (   12)
  covalent geometry    : bond        0.00224 ( 6753)
  covalent geometry    : angle       0.57725 ( 9177)

*********************** 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
  48 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.8966 (tp30) cc_final: 0.8666 (tm-30)
  outliers start: 6
  outliers final: 4
  residues processed: 48
  average time/residue: 0.2251
  time to fit residues: 15.4460
Evaluate side-chains
  42 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  530 CYS
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 70 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0060
   chunk 63 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.6396

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.058040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.045870 restraints weight = 51473.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 5.67
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4749

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= 0.109
  Angle     :  0.599   8.001   9234  Z= 0.287
  Chirality :  0.042   0.310    995
  Planarity :  0.003   0.028   1166
  Dihedral  :  6.092  54.634   1160
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.10 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.31), residues: 777
  helix:  1.57 (0.29), residues: 362
  sheet: -0.64 (0.88), residues: 31
  loop : -0.93 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 275 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.007   0.001   PHE A 230 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.002   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00288 (    8)
  link_NAG-ASN         : angle       2.73826 (   24)
  link_BETA1-4         : bond        0.01142 (    7)
  link_BETA1-4         : angle       2.46835 (   21)
  hydrogen bonds       : bond        0.03953 (  269)
  hydrogen bonds       : angle       4.16098 (  758)
  metal coordination   : bond        0.00114 (    2)
  SS BOND              : bond        0.00142 (    6)
  SS BOND              : angle       2.03242 (   12)
  covalent geometry    : bond        0.00237 ( 6753)
  covalent geometry    : angle       0.56709 ( 9177)

*********************** 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: 8
    poor density    : 41
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9161 (mmt) cc_final: 0.8932 (mmp)
REVERT: A  189 GLU cc_start: 0.8971 (tp30) cc_final: 0.8688 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1556
  time to fit residues: 11.4016
Evaluate side-chains
  42 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
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  530 CYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  477 ASN
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 59 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.057107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.044759 restraints weight = 58192.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 6.00
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.5015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6776  Z= 0.143
  Angle     :  0.641  11.650   9234  Z= 0.310
  Chirality :  0.044   0.325    995
  Planarity :  0.003   0.027   1166
  Dihedral  :  6.236  54.666   1160
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.32), residues: 777
  helix:  1.65 (0.29), residues: 363
  sheet: -1.27 (0.73), residues: 48
  loop : -0.74 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 610 
 HIS   0.011   0.001   HIS A 345 
 PHE   0.014   0.001   PHE A 230 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.004   0.000   ARG B 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00312 (    8)
  link_NAG-ASN         : angle       2.79140 (   24)
  link_BETA1-4         : bond        0.01025 (    7)
  link_BETA1-4         : angle       2.39294 (   21)
  hydrogen bonds       : bond        0.04236 (  269)
  hydrogen bonds       : angle       4.13394 (  758)
  metal coordination   : bond        0.00281 (    2)
  SS BOND              : bond        0.00283 (    6)
  SS BOND              : angle       2.29126 (   12)
  covalent geometry    : bond        0.00320 ( 6753)
  covalent geometry    : angle       0.61106 ( 9177)

*********************** 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: 9
    poor density    : 38
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9168 (mmt) cc_final: 0.8937 (mmp)
REVERT: A   82 MET cc_start: 0.7856 (ptm) cc_final: 0.7061 (ppp)
REVERT: A  189 GLU cc_start: 0.8961 (tp30) cc_final: 0.8713 (tm-30)
REVERT: A  360 MET cc_start: 0.8602 (mmm) cc_final: 0.8397 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 46
  average time/residue: 0.1433
  time to fit residues: 10.6735
Evaluate side-chains
  41 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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  530 CYS
Chi-restraints excluded: chain B residue  477 ASN
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 36 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.057221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.044519 restraints weight = 75003.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 6.75
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.5160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6776  Z= 0.127
  Angle     :  0.646  10.631   9234  Z= 0.313
  Chirality :  0.043   0.311    995
  Planarity :  0.003   0.030   1166
  Dihedral  :  6.236  54.547   1160
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.32), residues: 777
  helix:  1.53 (0.29), residues: 364
  sheet: -0.93 (0.76), residues: 46
  loop : -0.70 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 610 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.013   0.001   PHE A 230 
 TYR   0.013   0.001   TYR A  50 
 ARG   0.002   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    8)
  link_NAG-ASN         : angle       2.74062 (   24)
  link_BETA1-4         : bond        0.01080 (    7)
  link_BETA1-4         : angle       2.33867 (   21)
  hydrogen bonds       : bond        0.04176 (  269)
  hydrogen bonds       : angle       4.26198 (  758)
  metal coordination   : bond        0.00256 (    2)
  SS BOND              : bond        0.00455 (    6)
  SS BOND              : angle       2.57166 (   12)
  covalent geometry    : bond        0.00283 ( 6753)
  covalent geometry    : angle       0.61575 ( 9177)

*********************** 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
  44 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9179 (mmt) cc_final: 0.8963 (mmp)
REVERT: A   82 MET cc_start: 0.7996 (ptm) cc_final: 0.7094 (ppp)
REVERT: A  189 GLU cc_start: 0.8983 (tp30) cc_final: 0.8761 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 43
  average time/residue: 0.1365
  time to fit residues: 9.3129
Evaluate side-chains
  41 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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  530 CYS
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  477 ASN
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 61 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0970
   chunk 75 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.057258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.045010 restraints weight = 60533.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 5.95
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.5293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6776  Z= 0.121
  Angle     :  0.670  10.971   9234  Z= 0.319
  Chirality :  0.043   0.320    995
  Planarity :  0.003   0.026   1166
  Dihedral  :  6.257  54.542   1160
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.12 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.32), residues: 777
  helix:  1.53 (0.29), residues: 363
  sheet: -1.16 (0.72), residues: 46
  loop : -0.69 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 610 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.011   0.001   PHE A 230 
 TYR   0.012   0.001   TYR A  50 
 ARG   0.007   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00329 (    8)
  link_NAG-ASN         : angle       2.73582 (   24)
  link_BETA1-4         : bond        0.01037 (    7)
  link_BETA1-4         : angle       2.26428 (   21)
  hydrogen bonds       : bond        0.04116 (  269)
  hydrogen bonds       : angle       4.24467 (  758)
  metal coordination   : bond        0.00267 (    2)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       2.52459 (   12)
  covalent geometry    : bond        0.00271 ( 6753)
  covalent geometry    : angle       0.64145 ( 9177)

********************** 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
  41 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7965 (ptm) cc_final: 0.7133 (ppp)
REVERT: A  383 MET cc_start: 0.8935 (pmm) cc_final: 0.8701 (pmm)
  outliers start: 6
  outliers final: 6
  residues processed: 40
  average time/residue: 0.1467
  time to fit residues: 9.3513
Evaluate side-chains
  41 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
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  530 CYS
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  477 ASN
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 19 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0870
   chunk 76 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0170
   chunk 12 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.057629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.044857 restraints weight = 80538.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 6.96
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.5374

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= 0.111
  Angle     :  0.661  11.051   9234  Z= 0.316
  Chirality :  0.043   0.302    995
  Planarity :  0.003   0.026   1166
  Dihedral  :  6.226  54.474   1160
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 14.12 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.32), residues: 777
  helix:  1.52 (0.29), residues: 365
  sheet: -0.57 (0.75), residues: 41
  loop : -0.62 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 610 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 230 
 TYR   0.011   0.001   TYR A 158 
 ARG   0.003   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00321 (    8)
  link_NAG-ASN         : angle       2.64545 (   24)
  link_BETA1-4         : bond        0.01021 (    7)
  link_BETA1-4         : angle       2.22228 (   21)
  hydrogen bonds       : bond        0.03942 (  269)
  hydrogen bonds       : angle       4.23778 (  758)
  metal coordination   : bond        0.00109 (    2)
  SS BOND              : bond        0.00318 (    6)
  SS BOND              : angle       2.49456 (   12)
  covalent geometry    : bond        0.00244 ( 6753)
  covalent geometry    : angle       0.63439 ( 9177)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7632.65 seconds
wall clock time: 140 minutes 26.08 seconds (8426.08 seconds total)