Starting phenix.real_space_refine
on Mon Jul 28 19:55:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q4e_13804/07_2025/7q4e_13804_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q4e_13804/07_2025/7q4e_13804.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q4e_13804/07_2025/7q4e_13804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q4e_13804/07_2025/7q4e_13804.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q4e_13804/07_2025/7q4e_13804_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q4e_13804/07_2025/7q4e_13804_trim.cif"
  }
  resolution = 3.63
  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=   0.001 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      19      5.16       5
     C    3386      2.51       5
     N     868      2.21       5
     O    1044      1.98       5
     H    4731      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10049
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 9690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 608, 9690
          Classifications: {'peptide': 608}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 569}
    Chain: "C"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 85
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "B"
      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: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 64
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "F"
      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: "G"
      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: "H"
      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: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' ZN': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 6.03, per 1000 atoms: 0.60
  Number of scatterers: 10049
  At special positions: 0
  Unit cell: (86.92, 90.1, 93.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      19     16.00
     O    1044      8.00
     N     868      7.00
     C    3386      6.00
     H    4731      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 330 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 516 " - pdb=" SG  CYS A 528 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   6 "
      " BMA D   3 " - " MAN D   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   4 "
      " BMA E   3 " - " MAN E   4 "
    BETA1-2
      " MAN C   4 " - " NAG C   5 "
      " MAN E   4 " - " NAG E   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " 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 E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   7 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1302 " - " ASN A 416 "
      " NAG B   1 " - " ASN A 117 "
      " NAG C   1 " - " ASN A 289 "
      " NAG D   1 " - " ASN A  45 "
      " NAG E   1 " - " ASN A  25 "
      " NAG F   1 " - " ASN A 480 "
      " NAG G   1 " - " ASN A   9 "
      " NAG H   1 " - " ASN A  82 "
  Time building additional restraints: 3.63
  Conformation dependent library (CDL) restraints added in 611.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1301 "
        pdb="ZN    ZN A1301 " - pdb=" NE2 HIS A 365 "


  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1150

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      71.5% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 6
    Processing helix  chain 'A' and resid 13 through 45
      removed outlier: 3.518A  pdb=" N   LEU A  19 " --> pdb=" O   ALA A  15 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLN A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN A  34 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 77
      removed outlier: 3.914A  pdb=" N   LYS A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 85 through 96
    Processing helix  chain 'A' and resid 98 through 103
    Processing helix  chain 'A' and resid 104 through 124
    Processing helix  chain 'A' and resid 141 through 150
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 170 through 190
      removed outlier: 4.666A  pdb=" N   LEU A 174 " --> pdb=" O   PRO A 170 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLU A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN A 188 " --> pdb=" O   GLU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 201
      removed outlier: 3.742A  pdb=" N   TRP A 201 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 238
      removed outlier: 3.545A  pdb=" N   GLU A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      Proline residue:  A 220  - end of helix
      removed outlier: 3.539A  pdb=" N   GLY A 238 " --> pdb=" O   HIS A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 254
      removed outlier: 3.954A  pdb=" N   GLY A 254 " --> pdb=" O   HIS A 251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 251 through 254'
    Processing helix  chain 'A' and resid 261 through 263
      No H-bonds generated for 'chain 'A' and resid 261 through 263'
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 289 through 304
      removed outlier: 3.605A  pdb=" N   PHE A 294 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ARG A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 317
      removed outlier: 3.741A  pdb=" N   TRP A 314 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 373
      removed outlier: 3.611A  pdb=" N   HIS A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 386 through 401
      removed outlier: 4.305A  pdb=" N   LEU A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   THR A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 408
    Processing helix  chain 'A' and resid 417 through 433
    Processing helix  chain 'A' and resid 434 through 451
      removed outlier: 4.027A  pdb=" N   PHE A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASP A 443 " --> pdb=" O   GLY A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 471
    Processing helix  chain 'A' and resid 484 through 489
      removed outlier: 3.605A  pdb=" N   LYS A 489 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 519
      removed outlier: 3.684A  pdb=" N   PHE A 502 " --> pdb=" O   TYR A 498 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   PHE A 509 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA A 514 " --> pdb=" O   GLN A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
    Processing helix  chain 'A' and resid 533 through 547
      removed outlier: 3.561A  pdb=" N   LYS A 539 " --> pdb=" O   LYS A 535 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 561
    Processing helix  chain 'A' and resid 567 through 574
    Processing helix  chain 'A' and resid 574 through 589
    Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249
      removed outlier: 6.001A  pdb=" N   ILE A 248 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 336

    286 hydrogen bonds defined for protein.
    816 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: 3.54

  Time building geometry restraints manager: 4.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4730
        1.03 -     1.23: 24
        1.23 -     1.42: 2363
        1.42 -     1.62: 3057
        1.62 -     1.81: 31
  Bond restraints: 10205
  Sorted by residual:
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.32e+00
  bond pdb=" C1  NAG G   1 "
       pdb=" O5  NAG G   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.358  0.048 2.00e-02 2.50e+03 5.85e+00
  bond pdb=" C5  BMA D   3 "
       pdb=" O5  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.465 -0.048 2.00e-02 2.50e+03 5.74e+00
  bond pdb=" C2  BMA E   3 "
       pdb=" C3  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.544  1.497  0.047 2.00e-02 2.50e+03 5.49e+00
  bond pdb=" C1  MAN C   6 "
       pdb=" C2  MAN C   6 "
    ideal  model  delta    sigma   weight residual
    1.526  1.572 -0.046 2.00e-02 2.50e+03 5.34e+00
  ... (remaining 10200 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 17041
        1.43 -     2.87: 967
        2.87 -     4.30: 142
        4.30 -     5.74: 38
        5.74 -     7.17: 20
  Bond angle restraints: 18208
  Sorted by residual:
  angle pdb=" CA  ARG A 380 "
        pdb=" CB  ARG A 380 "
        pdb=" CG  ARG A 380 "
      ideal   model   delta    sigma   weight residual
     114.10  106.93    7.17 2.00e+00 2.50e-01 1.29e+01
  angle pdb=" CA  TYR A 372 "
        pdb=" CB  TYR A 372 "
        pdb=" CG  TYR A 372 "
      ideal   model   delta    sigma   weight residual
     113.90  120.13   -6.23 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" CA  GLU A 389 "
        pdb=" CB  GLU A 389 "
        pdb=" CG  GLU A 389 "
      ideal   model   delta    sigma   weight residual
     114.10  107.20    6.90 2.00e+00 2.50e-01 1.19e+01
  angle pdb=" C   HIS A 360 "
        pdb=" N   HIS A 361 "
        pdb=" CA  HIS A 361 "
      ideal   model   delta    sigma   weight residual
     120.29  116.10    4.19 1.42e+00 4.96e-01 8.71e+00
  angle pdb=" CB  ARG A 380 "
        pdb=" CG  ARG A 380 "
        pdb=" CD  ARG A 380 "
      ideal   model   delta    sigma   weight residual
     111.30  117.65   -6.35 2.30e+00 1.89e-01 7.61e+00
  ... (remaining 18203 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.18: 4797
       21.18 -    42.36: 275
       42.36 -    63.54: 115
       63.54 -    84.73: 48
       84.73 -   105.91: 29
  Dihedral angle restraints: 5264
    sinusoidal: 3029
      harmonic: 2235
  Sorted by residual:
  dihedral pdb=" CA  PRO A 604 "
           pdb=" C   PRO A 604 "
           pdb=" N   ASP A 605 "
           pdb=" CA  ASP A 605 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.90  -25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  ALA A 383 "
           pdb=" C   ALA A 383 "
           pdb=" N   ASN A 384 "
           pdb=" CA  ASN A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.94   24.06     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  CYS A 528 "
           pdb=" C   CYS A 528 "
           pdb=" N   ASP A 529 "
           pdb=" CA  ASP A 529 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.00   24.00     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 5261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 796
       0.092 -    0.184: 53
       0.184 -    0.276: 2
       0.276 -    0.368: 6
       0.368 -    0.461: 1
  Chirality restraints: 858
  Sorted by residual:
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN A  82 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.60    0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.58    0.30 2.00e-01 2.50e+01 2.32e+00
  ... (remaining 855 not shown)

  Planarity restraints: 1504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  96 "   -0.565 9.50e-02 1.11e+02   1.91e-01 5.27e+01
        pdb=" NE  ARG A  96 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  96 "    0.027 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  96 "   -0.046 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  96 "    0.035 2.00e-02 2.50e+03
        pdb="HH11 ARG A  96 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG A  96 "    0.041 2.00e-02 2.50e+03
        pdb="HH21 ARG A  96 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A  96 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 467 "   -0.562 9.50e-02 1.11e+02   1.89e-01 4.61e+01
        pdb=" NE  ARG A 467 "    0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 467 "   -0.035 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 467 "    0.024 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 467 "   -0.012 2.00e-02 2.50e+03
        pdb="HH11 ARG A 467 "    0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG A 467 "   -0.009 2.00e-02 2.50e+03
        pdb="HH21 ARG A 467 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 467 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 413 "    0.211 9.50e-02 1.11e+02   8.01e-02 3.75e+01
        pdb=" NE  ARG A 413 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 413 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 413 "   -0.080 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 413 "    0.011 2.00e-02 2.50e+03
        pdb="HH11 ARG A 413 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 413 "    0.074 2.00e-02 2.50e+03
        pdb="HH21 ARG A 413 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 413 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1501 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 1028
        2.25 -     2.83: 22011
        2.83 -     3.42: 26588
        3.42 -     4.01: 35815
        4.01 -     4.60: 55658
  Nonbonded interactions: 141100
  Sorted by model distance:
  nonbonded pdb=" HZ3 LYS A 107 "
            pdb=" OE2 GLU A 184 "
     model   vdw
     1.657 2.450
  nonbonded pdb=" OD2 ASP A 443 "
            pdb=" H   ILE A 499 "
     model   vdw
     1.667 2.450
  nonbonded pdb=" HE1 TRP A 464 "
            pdb=" OD2 ASP A 485 "
     model   vdw
     1.675 2.450
  nonbonded pdb=" HG1 THR A  47 "
            pdb=" OD1 ASN A  50 "
     model   vdw
     1.681 2.450
  nonbonded pdb=" O   PHE A  83 "
            pdb="HH11 ARG A  89 "
     model   vdw
     1.701 2.450
  ... (remaining 141095 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 'B'
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.180
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     30.590
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
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      :  0.008   0.054   5506  Z= 0.380
  Angle     :  1.058  13.493   7550  Z= 0.502
  Chirality :  0.057   0.461    858
  Planarity :  0.014   0.255    927
  Dihedral  : 19.121 105.908   2412
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.29), residues: 606
  helix: -1.32 (0.22), residues: 343
  sheet:  0.65 (1.57), residues: 10
  loop : -1.06 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP A  68 
 HIS   0.011   0.003   HIS A 234 
 PHE   0.024   0.003   PHE A 387 
 TYR   0.030   0.006   TYR A 372 
 ARG   0.042   0.005   ARG A 467 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00976 (    8)
  link_NAG-ASN         : angle       4.84772 (   24)
  link_ALPHA1-6        : bond        0.00082 (    2)
  link_ALPHA1-6        : angle       1.67961 (    6)
  link_BETA1-2         : bond        0.01097 (    2)
  link_BETA1-2         : angle       1.42918 (    6)
  link_BETA1-4         : bond        0.00737 (   13)
  link_BETA1-4         : angle       3.58617 (   39)
  link_ALPHA1-3        : bond        0.00800 (    2)
  link_ALPHA1-3        : angle       2.16397 (    6)
  hydrogen bonds       : bond        0.22354 (  286)
  hydrogen bonds       : angle       8.85943 (  816)
  link_BETA1-6         : bond        0.00258 (    1)
  link_BETA1-6         : angle       4.86683 (    3)
  metal coordination   : bond        0.04727 (    1)
  SS BOND              : bond        0.00499 (    3)
  SS BOND              : angle       1.54181 (    6)
  covalent geometry    : bond        0.00819 ( 5474)
  covalent geometry    : angle       0.98525 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.8416 (tpt) cc_final: 0.8089 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.4347
  time to fit residues: 55.1120
Evaluate side-chains
  52 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0010
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 24 optimal weight:    0.1980
   chunk 47 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 ASN
A 508 GLN
A 545 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.106069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.089938 restraints weight = 31045.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.093442 restraints weight = 12830.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.095722 restraints weight = 7094.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5506  Z= 0.167
  Angle     :  0.790   6.544   7550  Z= 0.387
  Chirality :  0.042   0.279    858
  Planarity :  0.006   0.055    927
  Dihedral  : 13.777  71.762   1233
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  7.27 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: 606
  helix:  0.18 (0.25), residues: 365
  sheet:  1.60 (1.56), residues: 10
  loop : -0.65 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 163 
 HIS   0.009   0.002   HIS A 365 
 PHE   0.021   0.002   PHE A 387 
 TYR   0.026   0.002   TYR A 372 
 ARG   0.004   0.001   ARG A 413 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00374 (    8)
  link_NAG-ASN         : angle       1.90427 (   24)
  link_ALPHA1-6        : bond        0.00543 (    2)
  link_ALPHA1-6        : angle       1.81534 (    6)
  link_BETA1-2         : bond        0.00428 (    2)
  link_BETA1-2         : angle       1.52709 (    6)
  link_BETA1-4         : bond        0.00436 (   13)
  link_BETA1-4         : angle       2.33268 (   39)
  link_ALPHA1-3        : bond        0.00986 (    2)
  link_ALPHA1-3        : angle       2.89376 (    6)
  hydrogen bonds       : bond        0.06683 (  286)
  hydrogen bonds       : angle       5.43766 (  816)
  link_BETA1-6         : bond        0.00172 (    1)
  link_BETA1-6         : angle       2.13942 (    3)
  metal coordination   : bond        0.00055 (    1)
  SS BOND              : bond        0.01205 (    3)
  SS BOND              : angle       2.60816 (    6)
  covalent geometry    : bond        0.00346 ( 5474)
  covalent geometry    : angle       0.75680 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.8262 (tpt) cc_final: 0.8034 (mmp)
  outliers start: 3
  outliers final: 3
  residues processed: 60
  average time/residue: 0.3805
  time to fit residues: 29.7041
Evaluate side-chains
  51 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  477 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0770
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.106290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.089777 restraints weight = 31730.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.093309 restraints weight = 13074.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.095618 restraints weight = 7297.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5506  Z= 0.150
  Angle     :  0.671   6.957   7550  Z= 0.325
  Chirality :  0.039   0.275    858
  Planarity :  0.005   0.046    927
  Dihedral  :  9.737  60.182   1233
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.37 %
    Favored  : 90.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.32), residues: 606
  helix:  0.79 (0.25), residues: 365
  sheet:  1.74 (1.68), residues: 10
  loop : -0.51 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 163 
 HIS   0.008   0.001   HIS A 361 
 PHE   0.014   0.002   PHE A 387 
 TYR   0.022   0.002   TYR A 372 
 ARG   0.002   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00226 (    8)
  link_NAG-ASN         : angle       1.51019 (   24)
  link_ALPHA1-6        : bond        0.00760 (    2)
  link_ALPHA1-6        : angle       1.58560 (    6)
  link_BETA1-2         : bond        0.00428 (    2)
  link_BETA1-2         : angle       1.00508 (    6)
  link_BETA1-4         : bond        0.00499 (   13)
  link_BETA1-4         : angle       2.05327 (   39)
  link_ALPHA1-3        : bond        0.01097 (    2)
  link_ALPHA1-3        : angle       1.87985 (    6)
  hydrogen bonds       : bond        0.05528 (  286)
  hydrogen bonds       : angle       5.00683 (  816)
  link_BETA1-6         : bond        0.00070 (    1)
  link_BETA1-6         : angle       1.80723 (    3)
  metal coordination   : bond        0.00074 (    1)
  SS BOND              : bond        0.00648 (    3)
  SS BOND              : angle       1.92929 (    6)
  covalent geometry    : bond        0.00321 ( 5474)
  covalent geometry    : angle       0.64572 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 53
  average time/residue: 0.2620
  time to fit residues: 20.3877
Evaluate side-chains
  45 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  590 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 251 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.105348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.088919 restraints weight = 31482.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.092395 restraints weight = 13063.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.094657 restraints weight = 7301.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5506  Z= 0.174
  Angle     :  0.654   6.525   7550  Z= 0.324
  Chirality :  0.039   0.264    858
  Planarity :  0.005   0.045    927
  Dihedral  :  8.022  45.922   1233
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.90 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.66 (0.33), residues: 606
  helix:  0.97 (0.26), residues: 368
  sheet:  1.65 (1.72), residues: 10
  loop : -0.38 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.013   0.002   HIS A 491 
 PHE   0.014   0.002   PHE A 387 
 TYR   0.022   0.002   TYR A 372 
 ARG   0.002   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00226 (    8)
  link_NAG-ASN         : angle       1.42289 (   24)
  link_ALPHA1-6        : bond        0.00962 (    2)
  link_ALPHA1-6        : angle       1.38977 (    6)
  link_BETA1-2         : bond        0.00282 (    2)
  link_BETA1-2         : angle       1.02738 (    6)
  link_BETA1-4         : bond        0.00334 (   13)
  link_BETA1-4         : angle       1.84535 (   39)
  link_ALPHA1-3        : bond        0.00971 (    2)
  link_ALPHA1-3        : angle       2.23849 (    6)
  hydrogen bonds       : bond        0.04992 (  286)
  hydrogen bonds       : angle       4.87915 (  816)
  link_BETA1-6         : bond        0.00031 (    1)
  link_BETA1-6         : angle       1.85079 (    3)
  metal coordination   : bond        0.00410 (    1)
  SS BOND              : bond        0.00890 (    3)
  SS BOND              : angle       1.03474 (    6)
  covalent geometry    : bond        0.00378 ( 5474)
  covalent geometry    : angle       0.63210 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7829 (mm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 49
  average time/residue: 0.2989
  time to fit residues: 20.7704
Evaluate side-chains
  45 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.106227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.089734 restraints weight = 31657.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.093248 restraints weight = 12964.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.095545 restraints weight = 7247.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5506  Z= 0.136
  Angle     :  0.604   6.624   7550  Z= 0.294
  Chirality :  0.037   0.253    858
  Planarity :  0.004   0.041    927
  Dihedral  :  7.168  57.548   1233
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.28 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.99 (0.33), residues: 606
  helix:  1.28 (0.26), residues: 368
  sheet:  1.22 (1.67), residues: 10
  loop : -0.31 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.007   0.001   HIS A 360 
 PHE   0.012   0.001   PHE A 511 
 TYR   0.020   0.002   TYR A 372 
 ARG   0.002   0.000   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00180 (    8)
  link_NAG-ASN         : angle       1.34119 (   24)
  link_ALPHA1-6        : bond        0.01032 (    2)
  link_ALPHA1-6        : angle       1.22061 (    6)
  link_BETA1-2         : bond        0.00294 (    2)
  link_BETA1-2         : angle       0.98391 (    6)
  link_BETA1-4         : bond        0.00371 (   13)
  link_BETA1-4         : angle       1.53024 (   39)
  link_ALPHA1-3        : bond        0.00953 (    2)
  link_ALPHA1-3        : angle       1.65615 (    6)
  hydrogen bonds       : bond        0.04719 (  286)
  hydrogen bonds       : angle       4.70363 (  816)
  link_BETA1-6         : bond        0.00227 (    1)
  link_BETA1-6         : angle       1.57041 (    3)
  metal coordination   : bond        0.00366 (    1)
  SS BOND              : bond        0.00134 (    3)
  SS BOND              : angle       0.96328 (    6)
  covalent geometry    : bond        0.00293 ( 5474)
  covalent geometry    : angle       0.58711 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7845 (mm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 49
  average time/residue: 0.2765
  time to fit residues: 19.8442
Evaluate side-chains
  47 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  498 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0270
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0040
   overall best weight:    0.4050

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.107217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.090822 restraints weight = 31307.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.094338 restraints weight = 12709.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.096668 restraints weight = 7088.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.4484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   5506  Z= 0.117
  Angle     :  0.562   6.107   7550  Z= 0.275
  Chirality :  0.035   0.230    858
  Planarity :  0.004   0.037    927
  Dihedral  :  6.056  47.588   1233
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.71 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.34), residues: 606
  helix:  1.46 (0.26), residues: 374
  sheet:  0.63 (1.57), residues: 10
  loop : -0.18 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.007   0.001   HIS A 361 
 PHE   0.010   0.001   PHE A 178 
 TYR   0.019   0.002   TYR A 372 
 ARG   0.002   0.000   ARG A 236 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00178 (    8)
  link_NAG-ASN         : angle       1.16298 (   24)
  link_ALPHA1-6        : bond        0.01181 (    2)
  link_ALPHA1-6        : angle       1.96043 (    6)
  link_BETA1-2         : bond        0.00291 (    2)
  link_BETA1-2         : angle       0.95989 (    6)
  link_BETA1-4         : bond        0.00306 (   13)
  link_BETA1-4         : angle       1.48050 (   39)
  link_ALPHA1-3        : bond        0.00892 (    2)
  link_ALPHA1-3        : angle       1.45732 (    6)
  hydrogen bonds       : bond        0.04374 (  286)
  hydrogen bonds       : angle       4.51381 (  816)
  link_BETA1-6         : bond        0.00220 (    1)
  link_BETA1-6         : angle       1.46174 (    3)
  metal coordination   : bond        0.00242 (    1)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.91699 (    6)
  covalent geometry    : bond        0.00250 ( 5474)
  covalent geometry    : angle       0.54460 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ASN cc_start: 0.7407 (t0) cc_final: 0.6717 (m-40)
REVERT: A  362 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7813 (mm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 52
  average time/residue: 0.3029
  time to fit residues: 21.7770
Evaluate side-chains
  49 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  590 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.106627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.090267 restraints weight = 31507.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.093724 restraints weight = 12752.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.096012 restraints weight = 7136.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5506  Z= 0.147
  Angle     :  0.581   5.710   7550  Z= 0.288
  Chirality :  0.035   0.237    858
  Planarity :  0.004   0.037    927
  Dihedral  :  5.893  45.458   1233
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.66 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.33), residues: 606
  helix:  1.47 (0.26), residues: 377
  sheet:  0.36 (1.51), residues: 10
  loop : -0.27 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.007   0.001   HIS A 404 
 PHE   0.011   0.001   PHE A 387 
 TYR   0.018   0.002   TYR A 372 
 ARG   0.003   0.000   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00224 (    8)
  link_NAG-ASN         : angle       1.19687 (   24)
  link_ALPHA1-6        : bond        0.01019 (    2)
  link_ALPHA1-6        : angle       1.68315 (    6)
  link_BETA1-2         : bond        0.00265 (    2)
  link_BETA1-2         : angle       1.03626 (    6)
  link_BETA1-4         : bond        0.00319 (   13)
  link_BETA1-4         : angle       1.48210 (   39)
  link_ALPHA1-3        : bond        0.00625 (    2)
  link_ALPHA1-3        : angle       1.38394 (    6)
  hydrogen bonds       : bond        0.04407 (  286)
  hydrogen bonds       : angle       4.51171 (  816)
  link_BETA1-6         : bond        0.00228 (    1)
  link_BETA1-6         : angle       1.56099 (    3)
  metal coordination   : bond        0.00414 (    1)
  SS BOND              : bond        0.00338 (    3)
  SS BOND              : angle       0.88653 (    6)
  covalent geometry    : bond        0.00324 ( 5474)
  covalent geometry    : angle       0.56546 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 1.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ASN cc_start: 0.7386 (t0) cc_final: 0.6786 (m-40)
  outliers start: 5
  outliers final: 5
  residues processed: 49
  average time/residue: 0.3151
  time to fit residues: 21.4322
Evaluate side-chains
  47 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  590 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.105926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.089458 restraints weight = 31280.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092962 restraints weight = 12821.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.095275 restraints weight = 7190.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5506  Z= 0.145
  Angle     :  0.572   5.386   7550  Z= 0.285
  Chirality :  0.035   0.231    858
  Planarity :  0.004   0.036    927
  Dihedral  :  5.751  43.576   1233
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.85 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.34), residues: 606
  helix:  1.50 (0.26), residues: 377
  sheet:  0.14 (1.46), residues: 10
  loop : -0.29 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.007   0.001   HIS A 361 
 PHE   0.038   0.002   PHE A 178 
 TYR   0.018   0.002   TYR A 372 
 ARG   0.003   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    8)
  link_NAG-ASN         : angle       1.15182 (   24)
  link_ALPHA1-6        : bond        0.01073 (    2)
  link_ALPHA1-6        : angle       1.75069 (    6)
  link_BETA1-2         : bond        0.00233 (    2)
  link_BETA1-2         : angle       0.99384 (    6)
  link_BETA1-4         : bond        0.00304 (   13)
  link_BETA1-4         : angle       1.46357 (   39)
  link_ALPHA1-3        : bond        0.00703 (    2)
  link_ALPHA1-3        : angle       1.37752 (    6)
  hydrogen bonds       : bond        0.04407 (  286)
  hydrogen bonds       : angle       4.48758 (  816)
  link_BETA1-6         : bond        0.00241 (    1)
  link_BETA1-6         : angle       1.50845 (    3)
  metal coordination   : bond        0.00429 (    1)
  SS BOND              : bond        0.00327 (    3)
  SS BOND              : angle       0.90209 (    6)
  covalent geometry    : bond        0.00317 ( 5474)
  covalent geometry    : angle       0.55636 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8331 (mtm-85)
REVERT: A  243 ASN cc_start: 0.7410 (t0) cc_final: 0.6775 (m-40)
  outliers start: 6
  outliers final: 4
  residues processed: 48
  average time/residue: 0.2575
  time to fit residues: 18.0918
Evaluate side-chains
  45 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  590 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.106526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.090123 restraints weight = 31306.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.093620 restraints weight = 12745.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.095951 restraints weight = 7137.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5506  Z= 0.128
  Angle     :  0.556   5.132   7550  Z= 0.276
  Chirality :  0.035   0.226    858
  Planarity :  0.004   0.033    927
  Dihedral  :  5.473  41.608   1233
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.24 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.34), residues: 606
  helix:  1.65 (0.26), residues: 377
  sheet: -0.11 (1.43), residues: 10
  loop : -0.35 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.007   0.001   HIS A 164 
 PHE   0.029   0.001   PHE A 178 
 TYR   0.026   0.002   TYR A 498 
 ARG   0.004   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00180 (    8)
  link_NAG-ASN         : angle       1.09088 (   24)
  link_ALPHA1-6        : bond        0.00997 (    2)
  link_ALPHA1-6        : angle       1.70676 (    6)
  link_BETA1-2         : bond        0.00290 (    2)
  link_BETA1-2         : angle       1.02801 (    6)
  link_BETA1-4         : bond        0.00305 (   13)
  link_BETA1-4         : angle       1.43005 (   39)
  link_ALPHA1-3        : bond        0.00700 (    2)
  link_ALPHA1-3        : angle       1.36474 (    6)
  hydrogen bonds       : bond        0.04282 (  286)
  hydrogen bonds       : angle       4.41781 (  816)
  link_BETA1-6         : bond        0.00264 (    1)
  link_BETA1-6         : angle       1.47567 (    3)
  metal coordination   : bond        0.00347 (    1)
  SS BOND              : bond        0.00119 (    3)
  SS BOND              : angle       0.86591 (    6)
  covalent geometry    : bond        0.00278 ( 5474)
  covalent geometry    : angle       0.54048 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ASN cc_start: 0.7418 (t0) cc_final: 0.7087 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 48
  average time/residue: 0.2914
  time to fit residues: 20.1814
Evaluate side-chains
  45 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  590 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0770
   chunk 47 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4536

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.107097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.090781 restraints weight = 31136.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.094309 restraints weight = 12618.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.096603 restraints weight = 7023.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5506  Z= 0.117
  Angle     :  0.544   4.810   7550  Z= 0.269
  Chirality :  0.034   0.220    858
  Planarity :  0.004   0.031    927
  Dihedral  :  5.218  40.192   1233
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.24 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.33), residues: 606
  helix:  1.77 (0.26), residues: 377
  sheet: -0.54 (1.37), residues: 10
  loop : -0.37 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 160 
 HIS   0.007   0.001   HIS A 361 
 PHE   0.022   0.001   PHE A 178 
 TYR   0.017   0.001   TYR A 372 
 ARG   0.003   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00175 (    8)
  link_NAG-ASN         : angle       1.06168 (   24)
  link_ALPHA1-6        : bond        0.01003 (    2)
  link_ALPHA1-6        : angle       1.70713 (    6)
  link_BETA1-2         : bond        0.00287 (    2)
  link_BETA1-2         : angle       1.02736 (    6)
  link_BETA1-4         : bond        0.00303 (   13)
  link_BETA1-4         : angle       1.41086 (   39)
  link_ALPHA1-3        : bond        0.00672 (    2)
  link_ALPHA1-3        : angle       1.36497 (    6)
  hydrogen bonds       : bond        0.04197 (  286)
  hydrogen bonds       : angle       4.36554 (  816)
  link_BETA1-6         : bond        0.00276 (    1)
  link_BETA1-6         : angle       1.45127 (    3)
  metal coordination   : bond        0.00258 (    1)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       0.80783 (    6)
  covalent geometry    : bond        0.00252 ( 5474)
  covalent geometry    : angle       0.52881 ( 7460)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ASN cc_start: 0.7442 (t0) cc_final: 0.7120 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 47
  average time/residue: 0.2917
  time to fit residues: 19.6585
Evaluate side-chains
  44 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  590 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.106265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.089987 restraints weight = 31020.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.093448 restraints weight = 12626.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.095747 restraints weight = 7072.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.5179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5506  Z= 0.158
  Angle     :  0.567   4.836   7550  Z= 0.284
  Chirality :  0.035   0.225    858
  Planarity :  0.004   0.030    927
  Dihedral  :  5.317  39.706   1233
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 12.43 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.33), residues: 606
  helix:  1.68 (0.26), residues: 378
  sheet: -0.66 (1.38), residues: 10
  loop : -0.39 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 160 
 HIS   0.012   0.001   HIS A 164 
 PHE   0.020   0.001   PHE A 178 
 TYR   0.017   0.002   TYR A 498 
 ARG   0.003   0.000   ARG A  89 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00224 (    8)
  link_NAG-ASN         : angle       1.11314 (   24)
  link_ALPHA1-6        : bond        0.00927 (    2)
  link_ALPHA1-6        : angle       1.62289 (    6)
  link_BETA1-2         : bond        0.00278 (    2)
  link_BETA1-2         : angle       1.09438 (    6)
  link_BETA1-4         : bond        0.00302 (   13)
  link_BETA1-4         : angle       1.45857 (   39)
  link_ALPHA1-3        : bond        0.00572 (    2)
  link_ALPHA1-3        : angle       1.43569 (    6)
  hydrogen bonds       : bond        0.04283 (  286)
  hydrogen bonds       : angle       4.43143 (  816)
  link_BETA1-6         : bond        0.00214 (    1)
  link_BETA1-6         : angle       1.49020 (    3)
  metal coordination   : bond        0.00515 (    1)
  SS BOND              : bond        0.00185 (    3)
  SS BOND              : angle       0.84592 (    6)
  covalent geometry    : bond        0.00350 ( 5474)
  covalent geometry    : angle       0.55140 ( 7460)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3846.37 seconds
wall clock time: 66 minutes 26.31 seconds (3986.31 seconds total)