Starting phenix.real_space_refine
on Wed Sep 17 06:29:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d32_46512/09_2025/9d32_46512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d32_46512/09_2025/9d32_46512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d32_46512/09_2025/9d32_46512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d32_46512/09_2025/9d32_46512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d32_46512/09_2025/9d32_46512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d32_46512/09_2025/9d32_46512.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.063
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      41      5.16       5
     C    3969      2.51       5
     N    1029      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6130
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4570
          Classifications: {'peptide': 584}
          Incomplete info: {'truncation_to_alanine': 85}
          Link IDs: {'PTRANS': 26, 'TRANS': 557}
          Unresolved non-hydrogen bonds: 227
          Unresolved non-hydrogen angles: 283
          Unresolved non-hydrogen dihedrals: 173
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 15, 'ASN:plan1': 4, 'GLN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 146
    Chain: "B"
      Number of atoms: 1423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1423
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 13, 'TRANS': 180}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 37
    Chain: "C"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 24
          Unusual residues: {'FUC': 1, 'NAG': 1}
          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: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 85
          Unusual residues: {' ZN': 1, 'NAG': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      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
  Time building chain proxies: 1.66, per 1000 atoms: 0.27
  Number of scatterers: 6130
  At special positions: 0
  Unit cell: (76, 84, 116, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      41     16.00
     O    1090      8.00
     N    1029      7.00
     C    3969      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 529 " - pdb=" SG  CYS A 541 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 392 " - pdb=" SG  CYS B 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 487 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 446 " - pdb=" SG  CYS B 584 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 512 " - pdb=" SG  CYS B 533 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-6
      " NAG C   1 " - " FUC C   2 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 801 " - " ASN A  53 "
      " NAG A 802 " - " ASN A 279 "
      " NAG A 803 " - " ASN A 431 "
      " NAG A 804 " - " ASN A 545 "
      " NAG A 805 " - " ASN A 103 "
      " NAG A 806 " - " ASN A 215 "
      " NAG B 701 " - " ASN B 419 "
      " NAG B 702 " - " ASN B 496 "
      " NAG C   1 " - " ASN A 386 "
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 319.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 807 "
        pdb="ZN    ZN A 807 " - pdb=" NE2 HIS A 377 "
        pdb="ZN    ZN A 807 " - pdb=" NE2 HIS A 373 "


  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1470

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      58.2% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 52
      removed outlier: 3.626A  pdb=" N   GLU A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ASN A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   HIS A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.812A  pdb=" N   ILE A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.536A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 101
      removed outlier: 3.523A  pdb=" N   ILE A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.738A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 129
    Processing helix  chain 'A' and resid 144 through 152
    Processing helix  chain 'A' and resid 156 through 171
      removed outlier: 3.684A  pdb=" N   VAL A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 193
      removed outlier: 3.601A  pdb=" N   GLU A 181 " --> pdb=" O   PRO A 177 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 184 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 204
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 220 through 251
      Proline residue:  A 234  - end of helix
      removed outlier: 3.804A  pdb=" N   LYS A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 266
      No H-bonds generated for 'chain 'A' and resid 264 through 266'
    Processing helix  chain 'A' and resid 274 through 276
      No H-bonds generated for 'chain 'A' and resid 274 through 276'
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 292 through 299
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.765A  pdb=" N   VAL A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 330
      removed outlier: 3.547A  pdb=" N   TRP A 327 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 384
      removed outlier: 3.668A  pdb=" N   HIS A 372 " --> pdb=" O   PHE A 368 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR A 384 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
      removed outlier: 3.578A  pdb=" N   ARG A 392 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 412
      removed outlier: 3.778A  pdb=" N   MET A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 421
    Processing helix  chain 'A' and resid 430 through 446
    Processing helix  chain 'A' and resid 448 through 465
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'A' and resid 471 through 483
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 512 through 532
      removed outlier: 4.018A  pdb=" N   THR A 518 " --> pdb=" O   TYR A 514 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 519 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A 527 " --> pdb=" O   GLN A 523 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 546 through 558
      removed outlier: 3.535A  pdb=" N   GLY A 550 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   MET A 556 " --> pdb=" O   LYS A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 574
      removed outlier: 3.766A  pdb=" N   ILE A 572 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 587
    Processing helix  chain 'A' and resid 587 through 599
      removed outlier: 3.544A  pdb=" N   GLU A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
    Processing helix  chain 'B' and resid 423 through 427
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 4.179A  pdb=" N   ALA B 443 " --> pdb=" O   PRO B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 465
      removed outlier: 4.652A  pdb=" N   SER B 463 " --> pdb=" O   ASP B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 477
    Processing helix  chain 'B' and resid 533 through 538
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.008A  pdb=" N   LEU A 261 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 349
    Processing sheet with id=AA4, first strand: chain 'B' and resid 409 through 413
      removed outlier: 6.863A  pdb=" N   THR B 486 " --> pdb=" O   CYS B 434 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   CYS B 434 " --> pdb=" O   THR B 486 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ARG B 488 " --> pdb=" O   PHE B 432 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   PHE B 432 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU B 490 " --> pdb=" O   SER B 430 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 522
      removed outlier: 6.530A  pdb=" N   THR B 556 " --> pdb=" O   THR B 510 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   CYS B 512 " --> pdb=" O   THR B 554 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR B 554 " --> pdb=" O   CYS B 512 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    870 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.99

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1905
        1.34 -     1.46: 1444
        1.46 -     1.58: 2882
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 6297
  Sorted by residual:
  bond pdb=" CA  VAL B 493 "
       pdb=" CB  VAL B 493 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.25e+00
  bond pdb=" N   VAL A 363 "
       pdb=" CA  VAL A 363 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.017 1.57e-02 4.06e+03 1.12e+00
  bond pdb=" CA  ASN A  53 "
       pdb=" C   ASN A  53 "
    ideal  model  delta    sigma   weight residual
    1.530  1.521  0.009 1.08e-02 8.57e+03 6.89e-01
  bond pdb=" C   GLU A  35 "
       pdb=" O   GLU A  35 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.29e-02 6.01e+03 6.84e-01
  bond pdb=" C1  FUC C   2 "
       pdb=" O5  FUC C   2 "
    ideal  model  delta    sigma   weight residual
    1.400  1.416 -0.016 2.00e-02 2.50e+03 6.68e-01
  ... (remaining 6292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 8277
        1.32 -     2.64: 223
        2.64 -     3.96: 57
        3.96 -     5.28: 10
        5.28 -     6.60: 2
  Bond angle restraints: 8569
  Sorted by residual:
  angle pdb=" N   VAL A 292 "
        pdb=" CA  VAL A 292 "
        pdb=" C   VAL A 292 "
      ideal   model   delta    sigma   weight residual
     112.43  110.06    2.37 9.20e-01 1.18e+00 6.62e+00
  angle pdb=" N   VAL A 363 "
        pdb=" CA  VAL A 363 "
        pdb=" C   VAL A 363 "
      ideal   model   delta    sigma   weight residual
     106.21  108.95   -2.74 1.07e+00 8.73e-01 6.56e+00
  angle pdb=" CA  CYS B 487 "
        pdb=" CB  CYS B 487 "
        pdb=" SG  CYS B 487 "
      ideal   model   delta    sigma   weight residual
     114.40  119.61   -5.21 2.30e+00 1.89e-01 5.14e+00
  angle pdb=" N   GLY B 557 "
        pdb=" CA  GLY B 557 "
        pdb=" C   GLY B 557 "
      ideal   model   delta    sigma   weight residual
     111.19  114.91   -3.72 1.75e+00 3.27e-01 4.52e+00
  angle pdb=" CA  TRP A 162 "
        pdb=" CB  TRP A 162 "
        pdb=" CG  TRP A 162 "
      ideal   model   delta    sigma   weight residual
     113.60  117.51   -3.91 1.90e+00 2.77e-01 4.23e+00
  ... (remaining 8564 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 3627
       17.52 -    35.04: 173
       35.04 -    52.55: 43
       52.55 -    70.07: 9
       70.07 -    87.59: 1
  Dihedral angle restraints: 3853
    sinusoidal: 1563
      harmonic: 2290
  Sorted by residual:
  dihedral pdb=" CB  CYS A 343 "
           pdb=" SG  CYS A 343 "
           pdb=" SG  CYS A 360 "
           pdb=" CB  CYS A 360 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.47  -50.47     1      1.00e+01 1.00e-02 3.49e+01
  dihedral pdb=" CB  CYS B 434 "
           pdb=" SG  CYS B 434 "
           pdb=" SG  CYS B 487 "
           pdb=" CB  CYS B 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -52.74  -33.26     1      1.00e+01 1.00e-02 1.57e+01
  dihedral pdb=" CA  ASN B 505 "
           pdb=" C   ASN B 505 "
           pdb=" N   TYR B 506 "
           pdb=" CA  TYR B 506 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.54   17.46     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 3850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 534
       0.029 -    0.058: 273
       0.058 -    0.087: 90
       0.087 -    0.116: 43
       0.116 -    0.145: 9
  Chirality restraints: 949
  Sorted by residual:
  chirality pdb=" C1  NAG B 702 "
            pdb=" ND2 ASN B 496 "
            pdb=" C2  NAG B 702 "
            pdb=" O5  NAG B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" C1  NAG A 805 "
            pdb=" ND2 ASN A 103 "
            pdb=" C2  NAG A 805 "
            pdb=" O5  NAG A 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  ILE B 571 "
            pdb=" N   ILE B 571 "
            pdb=" C   ILE B 571 "
            pdb=" CB  ILE B 571 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 946 not shown)

  Planarity restraints: 1093
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 233 "    0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO A 234 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 395 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.33e+00
        pdb=" N   PRO B 396 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B 396 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 396 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 581 "   -0.021 5.00e-02 4.00e+02   3.17e-02 1.60e+00
        pdb=" N   PRO A 582 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 582 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 582 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1090 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 25
        2.59 -     3.17: 4897
        3.17 -     3.74: 9077
        3.74 -     4.32: 12984
        4.32 -     4.90: 22356
  Nonbonded interactions: 49339
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 401 "
            pdb="ZN    ZN A 807 "
     model   vdw
     2.012 2.230
  nonbonded pdb=" OG  SER A 315 "
            pdb=" OD1 ASN A 321 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG  SER A 410 "
            pdb=" OD1 ASP A 542 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NH2 ARG B 410 "
            pdb=" O   GLY B 528 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OE1 GLU A 464 "
            pdb=" NZ  LYS A 466 "
     model   vdw
     2.378 3.120
  ... (remaining 49334 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.200
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.140
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
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      :  0.004   0.034   6316  Z= 0.174
  Angle     :  0.596   6.603   8613  Z= 0.332
  Chirality :  0.041   0.145    949
  Planarity :  0.004   0.043   1084
  Dihedral  : 11.073  87.590   2362
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  :  5.16 %
    Favored  : 91.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.30), residues: 772
  helix:  0.46 (0.27), residues: 383
  sheet:  1.58 (0.60), residues: 70
  loop :  0.62 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 392 
 TYR   0.014   0.001   TYR A 182 
 PHE   0.010   0.002   PHE A 307 
 TRP   0.014   0.001   TRP A 162 
 HIS   0.006   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6297)
  covalent geometry    : angle       0.58589 ( 8569)
  SS BOND              : bond        0.00263 (    7)
  SS BOND              : angle       1.33592 (   14)
  hydrogen bonds       : bond        0.17337 (  311)
  hydrogen bonds       : angle       6.59485 (  870)
  metal coordination   : bond        0.00244 (    2)
  link_BETA1-6         : bond        0.01215 (    1)
  link_BETA1-6         : angle       1.22720 (    3)
  link_NAG-ASN         : bond        0.00178 (    9)
  link_NAG-ASN         : angle       1.75779 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7733 (mmtt)
REVERT: A  159 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7240 (tt0)
REVERT: A  269 MET cc_start: 0.8748 (mmt) cc_final: 0.8500 (tpp)
REVERT: A  381 ASP cc_start: 0.8519 (m-30) cc_final: 0.8295 (m-30)
REVERT: A  400 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7030 (t-90)
REVERT: A  407 MET cc_start: 0.7186 (mmt) cc_final: 0.6951 (mmt)
REVERT: A  473 MET cc_start: 0.8475 (mmp) cc_final: 0.8031 (mmp)
REVERT: B  479 LYS cc_start: 0.8692 (tttm) cc_final: 0.7938 (ttmt)
REVERT: B  525 ASN cc_start: 0.7800 (m-40) cc_final: 0.7568 (m-40)
  outliers start: 17
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0928
  time to fit residues: 11.8713
Evaluate side-chains
  85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 372 HIS
B 436 GLN
B 565 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.137143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.111627 restraints weight = 6202.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.55
r_work: 0.3025 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6316  Z= 0.177
  Angle     :  0.568   6.319   8613  Z= 0.287
  Chirality :  0.042   0.152    949
  Planarity :  0.005   0.046   1084
  Dihedral  :  6.399  52.968   1070
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  :  9.25 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.30), residues: 772
  helix:  0.68 (0.26), residues: 385
  sheet:  1.77 (0.65), residues: 60
  loop :  0.44 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 328 
 TYR   0.014   0.002   TYR A 182 
 PHE   0.010   0.001   PHE A 307 
 TRP   0.013   0.001   TRP A 162 
 HIS   0.007   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 6297)
  covalent geometry    : angle       0.55527 ( 8569)
  SS BOND              : bond        0.00529 (    7)
  SS BOND              : angle       1.26291 (   14)
  hydrogen bonds       : bond        0.05876 (  311)
  hydrogen bonds       : angle       4.61305 (  870)
  metal coordination   : bond        0.00374 (    2)
  link_BETA1-6         : bond        0.01354 (    1)
  link_BETA1-6         : angle       1.24346 (    3)
  link_NAG-ASN         : bond        0.00206 (    9)
  link_NAG-ASN         : angle       2.00818 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7735 (mmtt)
REVERT: A  269 MET cc_start: 0.8693 (mmt) cc_final: 0.8357 (tpp)
REVERT: A  381 ASP cc_start: 0.8480 (m-30) cc_final: 0.8244 (m-30)
REVERT: A  400 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.7135 (t-90)
REVERT: A  407 MET cc_start: 0.7124 (mmt) cc_final: 0.6809 (mmt)
REVERT: A  473 MET cc_start: 0.8374 (mmp) cc_final: 0.7750 (mmp)
REVERT: B  479 LYS cc_start: 0.8718 (tttm) cc_final: 0.7981 (ttmt)
  outliers start: 15
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0991
  time to fit residues: 10.3649
Evaluate side-chains
  83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0970
   chunk 14 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
B 565 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.139950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.114439 restraints weight = 6139.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.55
r_work: 0.3068 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6316  Z= 0.114
  Angle     :  0.487   5.385   8613  Z= 0.244
  Chirality :  0.040   0.143    949
  Planarity :  0.004   0.039   1084
  Dihedral  :  5.686  52.280   1065
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  :  8.72 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.30), residues: 772
  helix:  1.05 (0.26), residues: 385
  sheet:  1.70 (0.65), residues: 60
  loop :  0.41 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 203 
 TYR   0.012   0.001   TYR A 182 
 PHE   0.007   0.001   PHE A 307 
 TRP   0.012   0.001   TRP A 162 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6297)
  covalent geometry    : angle       0.47553 ( 8569)
  SS BOND              : bond        0.00234 (    7)
  SS BOND              : angle       0.98915 (   14)
  hydrogen bonds       : bond        0.04633 (  311)
  hydrogen bonds       : angle       4.26975 (  870)
  metal coordination   : bond        0.00154 (    2)
  link_BETA1-6         : bond        0.01354 (    1)
  link_BETA1-6         : angle       1.26716 (    3)
  link_NAG-ASN         : bond        0.00161 (    9)
  link_NAG-ASN         : angle       1.78136 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  381 ASP cc_start: 0.8515 (m-30) cc_final: 0.8298 (m-30)
REVERT: A  400 HIS cc_start: 0.8483 (OUTLIER) cc_final: 0.6874 (t-90)
REVERT: A  407 MET cc_start: 0.7111 (mmt) cc_final: 0.6769 (mmt)
REVERT: A  473 MET cc_start: 0.8336 (mmp) cc_final: 0.7928 (mmp)
REVERT: B  472 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7799 (pm20)
REVERT: B  479 LYS cc_start: 0.8697 (tttm) cc_final: 0.7989 (ttmt)
REVERT: B  525 ASN cc_start: 0.7785 (m-40) cc_final: 0.7524 (m-40)
  outliers start: 18
  outliers final: 9
  residues processed: 93
  average time/residue: 0.1001
  time to fit residues: 11.8330
Evaluate side-chains
  90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  472 GLU
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 565 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.137034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.112823 restraints weight = 6177.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.53
r_work: 0.3052 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6316  Z= 0.161
  Angle     :  0.532   5.888   8613  Z= 0.268
  Chirality :  0.042   0.155    949
  Planarity :  0.004   0.038   1084
  Dihedral  :  5.842  53.579   1064
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 10.14 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.30), residues: 772
  helix:  0.94 (0.26), residues: 385
  sheet:  1.35 (0.66), residues: 61
  loop :  0.35 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 227 
 TYR   0.014   0.001   TYR A 182 
 PHE   0.010   0.001   PHE A 522 
 TRP   0.013   0.001   TRP A 162 
 HIS   0.007   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6297)
  covalent geometry    : angle       0.52133 ( 8569)
  SS BOND              : bond        0.00235 (    7)
  SS BOND              : angle       0.92141 (   14)
  hydrogen bonds       : bond        0.05372 (  311)
  hydrogen bonds       : angle       4.29606 (  870)
  metal coordination   : bond        0.00298 (    2)
  link_BETA1-6         : bond        0.01383 (    1)
  link_BETA1-6         : angle       1.27748 (    3)
  link_NAG-ASN         : bond        0.00176 (    9)
  link_NAG-ASN         : angle       1.85992 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.7018 (t-90)
REVERT: A  407 MET cc_start: 0.7332 (mmt) cc_final: 0.6951 (mmt)
REVERT: B  479 LYS cc_start: 0.8765 (tttm) cc_final: 0.8042 (ttmt)
  outliers start: 16
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0963
  time to fit residues: 9.9434
Evaluate side-chains
  82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  454 MET
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 72 optimal weight:    0.0770
   chunk 61 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.139268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.114039 restraints weight = 6291.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.54
r_work: 0.3066 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6316  Z= 0.116
  Angle     :  0.485   5.208   8613  Z= 0.243
  Chirality :  0.040   0.150    949
  Planarity :  0.004   0.034   1084
  Dihedral  :  5.632  53.249   1064
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  :  9.96 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.30), residues: 772
  helix:  1.14 (0.26), residues: 385
  sheet:  1.35 (0.67), residues: 61
  loop :  0.42 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.012   0.001   TYR A 182 
 PHE   0.008   0.001   PHE A 307 
 TRP   0.013   0.001   TRP A 162 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6297)
  covalent geometry    : angle       0.47474 ( 8569)
  SS BOND              : bond        0.00196 (    7)
  SS BOND              : angle       0.70651 (   14)
  hydrogen bonds       : bond        0.04584 (  311)
  hydrogen bonds       : angle       4.15672 (  870)
  metal coordination   : bond        0.00171 (    2)
  link_BETA1-6         : bond        0.01273 (    1)
  link_BETA1-6         : angle       1.27280 (    3)
  link_NAG-ASN         : bond        0.00181 (    9)
  link_NAG-ASN         : angle       1.76570 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.6892 (t-90)
REVERT: A  473 MET cc_start: 0.8290 (mmp) cc_final: 0.7989 (mmp)
REVERT: B  479 LYS cc_start: 0.8718 (tttm) cc_final: 0.7994 (ttmt)
REVERT: B  525 ASN cc_start: 0.7868 (m-40) cc_final: 0.7624 (m-40)
  outliers start: 19
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0829
  time to fit residues: 9.7518
Evaluate side-chains
  89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Chi-restraints excluded: chain B residue  505 ASN
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0770
   chunk 66 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.136289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.110801 restraints weight = 6226.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.57
r_work: 0.3020 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6316  Z= 0.181
  Angle     :  0.557   6.032   8613  Z= 0.280
  Chirality :  0.042   0.161    949
  Planarity :  0.004   0.038   1084
  Dihedral  :  5.716  54.823   1061
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.57 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.30), residues: 772
  helix:  0.89 (0.26), residues: 391
  sheet:  1.19 (0.67), residues: 61
  loop :  0.32 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 227 
 TYR   0.014   0.002   TYR A 182 
 PHE   0.011   0.002   PHE A 522 
 TRP   0.012   0.001   TRP A 162 
 HIS   0.008   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 6297)
  covalent geometry    : angle       0.54605 ( 8569)
  SS BOND              : bond        0.00260 (    7)
  SS BOND              : angle       1.22473 (   14)
  hydrogen bonds       : bond        0.05618 (  311)
  hydrogen bonds       : angle       4.28512 (  870)
  metal coordination   : bond        0.00367 (    2)
  link_BETA1-6         : bond        0.01318 (    1)
  link_BETA1-6         : angle       1.27060 (    3)
  link_NAG-ASN         : bond        0.00197 (    9)
  link_NAG-ASN         : angle       1.87943 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7248 (tt0)
REVERT: A  400 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.6647 (t-90)
REVERT: A  473 MET cc_start: 0.8382 (mmp) cc_final: 0.7972 (mmp)
REVERT: B  479 LYS cc_start: 0.8724 (tttm) cc_final: 0.7929 (ttmt)
  outliers start: 14
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0903
  time to fit residues: 9.2701
Evaluate side-chains
  83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 55 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 19 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.139113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.113099 restraints weight = 6175.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.61
r_work: 0.3052 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6316  Z= 0.116
  Angle     :  0.494   5.283   8613  Z= 0.246
  Chirality :  0.040   0.149    949
  Planarity :  0.004   0.034   1084
  Dihedral  :  5.476  54.278   1061
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 11.92 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.31), residues: 772
  helix:  1.10 (0.26), residues: 391
  sheet:  1.19 (0.67), residues: 61
  loop :  0.37 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.012   0.001   TYR A 182 
 PHE   0.008   0.001   PHE A 451 
 TRP   0.013   0.001   TRP A 162 
 HIS   0.004   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6297)
  covalent geometry    : angle       0.48283 ( 8569)
  SS BOND              : bond        0.00184 (    7)
  SS BOND              : angle       0.89541 (   14)
  hydrogen bonds       : bond        0.04572 (  311)
  hydrogen bonds       : angle       4.16444 (  870)
  metal coordination   : bond        0.00163 (    2)
  link_BETA1-6         : bond        0.01326 (    1)
  link_BETA1-6         : angle       1.29558 (    3)
  link_NAG-ASN         : bond        0.00180 (    9)
  link_NAG-ASN         : angle       1.78922 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7711 (mmtt)
REVERT: A  170 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7340 (mt-10)
REVERT: A  400 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.6733 (t-90)
REVERT: A  473 MET cc_start: 0.8304 (mmp) cc_final: 0.7946 (mmp)
REVERT: B  475 GLN cc_start: 0.8420 (mt0) cc_final: 0.8198 (mt0)
REVERT: B  479 LYS cc_start: 0.8751 (tttm) cc_final: 0.8004 (ttmt)
  outliers start: 15
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0882
  time to fit residues: 10.2295
Evaluate side-chains
  91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 72 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.138995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.113617 restraints weight = 6196.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.55
r_work: 0.3058 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6316  Z= 0.121
  Angle     :  0.493   5.316   8613  Z= 0.247
  Chirality :  0.040   0.149    949
  Planarity :  0.004   0.034   1084
  Dihedral  :  5.456  54.294   1061
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 12.63 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.31), residues: 772
  helix:  1.14 (0.26), residues: 391
  sheet:  1.22 (0.67), residues: 61
  loop :  0.38 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 227 
 TYR   0.013   0.001   TYR A 182 
 PHE   0.009   0.001   PHE A 522 
 TRP   0.013   0.001   TRP A 162 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6297)
  covalent geometry    : angle       0.48279 ( 8569)
  SS BOND              : bond        0.00193 (    7)
  SS BOND              : angle       0.78101 (   14)
  hydrogen bonds       : bond        0.04618 (  311)
  hydrogen bonds       : angle       4.13871 (  870)
  metal coordination   : bond        0.00177 (    2)
  link_BETA1-6         : bond        0.01311 (    1)
  link_BETA1-6         : angle       1.29334 (    3)
  link_NAG-ASN         : bond        0.00176 (    9)
  link_NAG-ASN         : angle       1.75792 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7725 (mmtt)
REVERT: A  400 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.6759 (t-90)
REVERT: A  473 MET cc_start: 0.8325 (mmp) cc_final: 0.7933 (mmp)
REVERT: A  478 GLU cc_start: 0.8289 (tt0) cc_final: 0.7778 (mt-10)
REVERT: A  530 ARG cc_start: 0.7334 (ttp-110) cc_final: 0.6951 (ttp80)
REVERT: B  479 LYS cc_start: 0.8746 (tttm) cc_final: 0.8015 (ttmt)
  outliers start: 14
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0850
  time to fit residues: 9.6111
Evaluate side-chains
  91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0870
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    0.2980
   overall best weight:    0.3496

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.140726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.115271 restraints weight = 6239.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.58
r_work: 0.3079 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6316  Z= 0.104
  Angle     :  0.470   4.970   8613  Z= 0.235
  Chirality :  0.039   0.141    949
  Planarity :  0.004   0.033   1084
  Dihedral  :  5.334  54.003   1061
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 12.81 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.31), residues: 772
  helix:  1.32 (0.26), residues: 390
  sheet:  1.29 (0.68), residues: 61
  loop :  0.42 (0.37), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 227 
 TYR   0.012   0.001   TYR A 182 
 PHE   0.008   0.001   PHE A 307 
 TRP   0.014   0.001   TRP A 162 
 HIS   0.004   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6297)
  covalent geometry    : angle       0.46048 ( 8569)
  SS BOND              : bond        0.00167 (    7)
  SS BOND              : angle       0.70160 (   14)
  hydrogen bonds       : bond        0.04194 (  311)
  hydrogen bonds       : angle       4.06961 (  870)
  metal coordination   : bond        0.00123 (    2)
  link_BETA1-6         : bond        0.01263 (    1)
  link_BETA1-6         : angle       1.30815 (    3)
  link_NAG-ASN         : bond        0.00174 (    9)
  link_NAG-ASN         : angle       1.68399 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8167 (mmtp) cc_final: 0.7715 (mmtt)
REVERT: A  400 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.6675 (t-90)
REVERT: A  473 MET cc_start: 0.8286 (mmp) cc_final: 0.7906 (mmp)
REVERT: A  478 GLU cc_start: 0.8280 (tt0) cc_final: 0.7784 (mt-10)
REVERT: A  508 ASP cc_start: 0.8580 (t0) cc_final: 0.8216 (t0)
REVERT: A  530 ARG cc_start: 0.7345 (ttp-110) cc_final: 0.6949 (ttp80)
REVERT: B  479 LYS cc_start: 0.8723 (tttm) cc_final: 0.8002 (ttmt)
  outliers start: 14
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0842
  time to fit residues: 9.5386
Evaluate side-chains
  91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0020
   chunk 28 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 42 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 567 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.139079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.116093 restraints weight = 6242.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.65
r_work: 0.3059 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6316  Z= 0.126
  Angle     :  0.497   5.279   8613  Z= 0.249
  Chirality :  0.040   0.143    949
  Planarity :  0.004   0.034   1084
  Dihedral  :  5.449  54.308   1061
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.17 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.31), residues: 772
  helix:  1.28 (0.26), residues: 390
  sheet:  1.20 (0.67), residues: 61
  loop :  0.38 (0.37), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 328 
 TYR   0.013   0.001   TYR A 182 
 PHE   0.009   0.001   PHE A 522 
 TRP   0.013   0.001   TRP A 162 
 HIS   0.006   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6297)
  covalent geometry    : angle       0.48723 ( 8569)
  SS BOND              : bond        0.00192 (    7)
  SS BOND              : angle       0.70408 (   14)
  hydrogen bonds       : bond        0.04635 (  311)
  hydrogen bonds       : angle       4.12253 (  870)
  metal coordination   : bond        0.00197 (    2)
  link_BETA1-6         : bond        0.01248 (    1)
  link_BETA1-6         : angle       1.29563 (    3)
  link_NAG-ASN         : bond        0.00173 (    9)
  link_NAG-ASN         : angle       1.71036 (   27)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7701 (mmtt)
REVERT: A  400 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.6762 (t-90)
REVERT: A  473 MET cc_start: 0.8327 (mmp) cc_final: 0.7929 (mmp)
REVERT: A  478 GLU cc_start: 0.8293 (tt0) cc_final: 0.7784 (mt-10)
REVERT: A  530 ARG cc_start: 0.7354 (ttp-110) cc_final: 0.6954 (ttp80)
REVERT: B  479 LYS cc_start: 0.8729 (tttm) cc_final: 0.7988 (ttmt)
  outliers start: 12
  outliers final: 11
  residues processed: 85
  average time/residue: 0.0841
  time to fit residues: 9.3308
Evaluate side-chains
  88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  513 ARG
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  487 CYS
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.138703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.113435 restraints weight = 6129.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.55
r_work: 0.3055 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6316  Z= 0.131
  Angle     :  0.506   5.443   8613  Z= 0.253
  Chirality :  0.040   0.142    949
  Planarity :  0.004   0.034   1084
  Dihedral  :  5.517  54.422   1061
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.99 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.31), residues: 772
  helix:  1.24 (0.26), residues: 390
  sheet:  1.19 (0.67), residues: 61
  loop :  0.36 (0.37), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 328 
 TYR   0.013   0.001   TYR A 182 
 PHE   0.009   0.001   PHE A 522 
 TRP   0.012   0.001   TRP A 162 
 HIS   0.006   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6297)
  covalent geometry    : angle       0.49573 ( 8569)
  SS BOND              : bond        0.00195 (    7)
  SS BOND              : angle       0.69314 (   14)
  hydrogen bonds       : bond        0.04752 (  311)
  hydrogen bonds       : angle       4.14022 (  870)
  metal coordination   : bond        0.00212 (    2)
  link_BETA1-6         : bond        0.01221 (    1)
  link_BETA1-6         : angle       1.28659 (    3)
  link_NAG-ASN         : bond        0.00240 (    9)
  link_NAG-ASN         : angle       1.81110 (   27)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1699.77 seconds
wall clock time: 29 minutes 44.21 seconds (1784.21 seconds total)