Starting phenix.real_space_refine
on Sun Apr 27 14:49:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bvq_44941/04_2025/9bvq_44941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bvq_44941/04_2025/9bvq_44941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bvq_44941/04_2025/9bvq_44941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bvq_44941/04_2025/9bvq_44941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bvq_44941/04_2025/9bvq_44941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bvq_44941/04_2025/9bvq_44941.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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
     P       2      5.49       5
     S      25      5.16       5
     C    3906      2.51       5
     N     977      2.21       5
     O    1067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5977
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5490
          Classifications: {'peptide': 665}
          Link IDs: {'PTRANS': 35, 'TRANS': 629}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 293
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 2, 'TRANS': 32}
          Chain breaks: 1
    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
    Chain: "C"
      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: "D"
      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: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 110
          Unusual residues: {'6PL': 2, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   6PL A 801 " occ=0.60
      ... (44 atoms not shown)
      pdb=" P   6PL A 801 " occ=0.60
    residue:
      pdb=" N   6PL A 802 " occ=0.60
      ... (48 atoms not shown)
      pdb=" P   6PL A 802 " occ=0.60
  Time building chain proxies: 4.27, per 1000 atoms: 0.71
  Number of scatterers: 5977
  At special positions: 0
  Unit cell: (86.7626, 85.8773, 108.896, 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)
     S      25     16.00
     P       2     15.00
     O    1067      8.00
     N     977      7.00
     C    3906      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 450 " 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
      
  Atom "HETATM 5851  O5  NAG D   1 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 803 " - " ASN A 459 "
      " NAG B   1 " - " ASN A 570 "
      " NAG C   1 " - " ASN A 550 "
      " NAG D   1 " - " ASN A 605 "
  Time building additional restraints: 1.56
  Conformation dependent library (CDL) restraints added in 784.4 milliseconds
  

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      55.3% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
    Processing helix  chain 'A' and resid 41 through 46
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 61 through 79
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.537A  pdb=" N   LYS A  91 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 132
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 145  - end of helix
      removed outlier: 3.747A  pdb=" N   ASP A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 157
      removed outlier: 3.777A  pdb=" N   TRP A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 154 through 157'
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 4.209A  pdb=" N   PHE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 174 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.509A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 218
      removed outlier: 3.776A  pdb=" N   LEU A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 244
      removed outlier: 3.863A  pdb=" N   LEU A 232 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   SER A 233 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 234 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS A 235 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   TRP A 236 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
    Processing helix  chain 'A' and resid 246 through 254
    Processing helix  chain 'A' and resid 256 through 270
      removed outlier: 4.024A  pdb=" N   LEU A 270 " --> pdb=" O   ALA A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 294
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 308 through 311
    Processing helix  chain 'A' and resid 314 through 321
      removed outlier: 3.823A  pdb=" N   LYS A 318 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 319 " --> pdb=" O   TRP A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 377
      removed outlier: 3.539A  pdb=" N   ALA A 364 " --> pdb=" O   HIS A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 380
      No H-bonds generated for 'chain 'A' and resid 378 through 380'
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.700A  pdb=" N   TYR A 387 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 455
    Processing helix  chain 'A' and resid 456 through 459
      removed outlier: 3.596A  pdb=" N   ASN A 459 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 456 through 459'
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 4.111A  pdb=" N   LYS A 515 " --> pdb=" O   PRO A 511 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLN A 517 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 627
    Processing helix  chain 'A' and resid 638 through 644
    Processing helix  chain 'A' and resid 653 through 674
    Processing helix  chain 'A' and resid 676 through 709
      removed outlier: 3.598A  pdb=" N   ARG A 680 " --> pdb=" O   PRO A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 724
    Processing helix  chain 'P' and resid 33 through 38
      removed outlier: 3.725A  pdb=" N   GLN P  38 " --> pdb=" O   PRO P  34 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 479 through 480
      removed outlier: 3.661A  pdb=" N   GLN A 479 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   HIS A 410 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   SER A 472 " --> pdb=" O   HIS A 408 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   HIS A 408 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ILE A 413 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   TYR A 425 " --> pdb=" O   LEU P  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 534
      removed outlier: 6.573A  pdb=" N   CYS A 598 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   THR A 551 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.614A  pdb=" N   VAL A 560 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)

    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: 1.55

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1008
        1.33 -     1.45: 1734
        1.45 -     1.57: 3357
        1.57 -     1.69: 4
        1.69 -     1.81: 42
  Bond restraints: 6145
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.77e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.41e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.35e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.35e+00
  ... (remaining 6140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 8109
        1.21 -     2.42: 167
        2.42 -     3.63: 45
        3.63 -     4.84: 5
        4.84 -     6.04: 4
  Bond angle restraints: 8330
  Sorted by residual:
  angle pdb=" N   VAL P  30 "
        pdb=" CA  VAL P  30 "
        pdb=" C   VAL P  30 "
      ideal   model   delta    sigma   weight residual
     112.96  110.14    2.82 1.00e+00 1.00e+00 7.97e+00
  angle pdb=" N   PRO P  34 "
        pdb=" CA  PRO P  34 "
        pdb=" C   PRO P  34 "
      ideal   model   delta    sigma   weight residual
     110.70  113.08   -2.38 1.22e+00 6.72e-01 3.80e+00
  angle pdb=" CA  PRO P  34 "
        pdb=" C   PRO P  34 "
        pdb=" N   PRO P  35 "
      ideal   model   delta    sigma   weight residual
     117.93  120.18   -2.25 1.20e+00 6.94e-01 3.51e+00
  angle pdb=" CA  VAL P  30 "
        pdb=" C   VAL P  30 "
        pdb=" O   VAL P  30 "
      ideal   model   delta    sigma   weight residual
     119.29  120.74   -1.45 8.40e-01 1.42e+00 2.99e+00
  angle pdb=" N   PHE A 268 "
        pdb=" CA  PHE A 268 "
        pdb=" C   PHE A 268 "
      ideal   model   delta    sigma   weight residual
     112.90  115.13   -2.23 1.31e+00 5.83e-01 2.89e+00
  ... (remaining 8325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.96: 3573
       24.96 -    49.92: 96
       49.92 -    74.88: 27
       74.88 -    99.85: 8
       99.85 -   124.81: 17
  Dihedral angle restraints: 3721
    sinusoidal: 1670
      harmonic: 2051
  Sorted by residual:
  dihedral pdb=" C2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   61.85 -124.81     1      3.00e+01 1.11e-03 1.68e+01
  dihedral pdb=" C1  NAG C   1 "
           pdb=" C5  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C6  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -68.78 -120.06     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" C1  NAG C   1 "
           pdb=" C5  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C4  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   55.88 -119.99     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 3718 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.332: 898
       0.332 -    0.664: 2
       0.664 -    0.996: 3
       0.996 -    1.329: 0
       1.329 -    1.661: 2
  Chirality restraints: 905
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.02   -1.38 2.00e-02 2.50e+03 4.73e+03
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.48   -0.92 2.00e-02 2.50e+03 2.13e+03
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.70   -0.70 2.00e-02 2.50e+03 1.21e+03
  ... (remaining 902 not shown)

  Planarity restraints: 1038
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 570 "    0.003 2.00e-02 2.50e+03   5.51e-02 3.79e+01
        pdb=" CG  ASN A 570 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 570 "   -0.050 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 570 "    0.094 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 550 "   -0.046 2.00e-02 2.50e+03   5.28e-02 3.49e+01
        pdb=" CG  ASN A 550 "    0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 550 "    0.015 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 550 "    0.080 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 459 "   -0.008 2.00e-02 2.50e+03   1.90e-02 4.51e+00
        pdb=" CG  ASN A 459 "    0.005 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 459 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 459 "    0.034 2.00e-02 2.50e+03
        pdb=" C1  NAG A 803 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1035 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 460
        2.74 -     3.28: 5532
        3.28 -     3.82: 9313
        3.82 -     4.36: 10638
        4.36 -     4.90: 19258
  Nonbonded interactions: 45201
  Sorted by model distance:
  nonbonded pdb=" O   ASP A  60 "
            pdb=" OH  TYR A 200 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   SER A 228 "
            pdb=" NE2 HIS A 256 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OD2 ASP A 153 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" NH1 ARG A 704 "
            pdb=" OE2 GLU A 719 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" OD1 ASP A 417 "
            pdb=" OG1 THR A 461 "
     model   vdw
     2.351 3.040
  ... (remaining 45196 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 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.60 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.500
  Find NCS groups from input model:        0.060
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
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   0.200   6153  Z= 0.210
  Angle     :  1.392  55.479   8353  Z= 0.496
  Chirality :  0.096   1.661    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 15.642 124.808   2398
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  4.59 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.89 (0.33), residues: 692
  helix:  1.34 (0.28), residues: 348
  sheet:  1.62 (0.58), residues: 73
  loop : -0.65 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 590 
 ARG   0.001   0.000   ARG A 406 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.11272 (    4)
  link_NAG-ASN         : angle      24.34865 (   12)
  link_BETA1-4         : bond        0.06797 (    3)
  link_BETA1-4         : angle      28.34613 (    9)
  hydrogen bonds       : bond        0.13855 (  286)
  hydrogen bonds       : angle       5.67442 (  816)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.42604 (    2)
  covalent geometry    : bond        0.00273 ( 6145)
  covalent geometry    : angle       0.47055 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8528 (mt) cc_final: 0.8313 (mp)
REVERT: A  115 MET cc_start: 0.8407 (mmt) cc_final: 0.7898 (mmt)
REVERT: A  180 TRP cc_start: 0.7480 (t60) cc_final: 0.7112 (t-100)
REVERT: A  680 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.6993 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6959 (p90)
  outliers start: 10
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2958
  time to fit residues: 40.9913
Evaluate side-chains
  59 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0570
   chunk 27 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0010
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5304

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

Flipped N/Q/H residues before XYZ refinement:
P  38 GLN
P  44 HIS
P  97 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.133375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.096112 restraints weight = 9210.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.68
r_work: 0.3069 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6153  Z= 0.125
  Angle     :  0.660  11.560   8353  Z= 0.291
  Chirality :  0.042   0.290    905
  Planarity :  0.005   0.049   1034
  Dihedral  : 14.584  78.581   1011
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  6.96 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.48 (0.34), residues: 692
  helix:  1.82 (0.29), residues: 355
  sheet:  1.73 (0.58), residues: 73
  loop : -0.37 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 315 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.010   0.001   TYR A 285 
 ARG   0.006   0.001   ARG A 671 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00761 (    4)
  link_NAG-ASN         : angle       6.34372 (   12)
  link_BETA1-4         : bond        0.00920 (    3)
  link_BETA1-4         : angle       2.23903 (    9)
  hydrogen bonds       : bond        0.04197 (  286)
  hydrogen bonds       : angle       4.17342 (  816)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.23362 (    2)
  covalent geometry    : bond        0.00278 ( 6145)
  covalent geometry    : angle       0.61135 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8627 (mmp) cc_final: 0.8418 (mmp)
REVERT: A  180 TRP cc_start: 0.7817 (t60) cc_final: 0.7265 (t-100)
REVERT: A  663 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8489 (tp-100)
REVERT: A  680 ARG cc_start: 0.7736 (mtp-110) cc_final: 0.6862 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6752 (p90)
  outliers start: 6
  outliers final: 1
  residues processed: 65
  average time/residue: 0.2619
  time to fit residues: 21.6368
Evaluate side-chains
  57 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 6 optimal weight:    0.0570
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.132706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.095253 restraints weight = 9248.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.74
r_work: 0.2993 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6153  Z= 0.111
  Angle     :  0.571   7.868   8353  Z= 0.260
  Chirality :  0.041   0.237    905
  Planarity :  0.004   0.050   1034
  Dihedral  : 12.553  76.306   1011
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  7.44 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.72 (0.34), residues: 692
  helix:  2.06 (0.29), residues: 355
  sheet:  1.80 (0.58), residues: 73
  loop : -0.32 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.006   0.001   HIS P  44 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.015   0.001   TYR A 285 
 ARG   0.006   0.000   ARG A 671 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00833 (    4)
  link_NAG-ASN         : angle       4.76509 (   12)
  link_BETA1-4         : bond        0.00606 (    3)
  link_BETA1-4         : angle       1.81130 (    9)
  hydrogen bonds       : bond        0.03855 (  286)
  hydrogen bonds       : angle       3.91646 (  816)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.13124 (    2)
  covalent geometry    : bond        0.00242 ( 6145)
  covalent geometry    : angle       0.53889 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.9072 (tppt) cc_final: 0.8841 (tppt)
REVERT: A  180 TRP cc_start: 0.7832 (t60) cc_final: 0.7240 (t-100)
REVERT: A  183 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8147 (m-30)
REVERT: A  619 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8599 (tm-30)
REVERT: A  663 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8526 (tp-100)
REVERT: A  680 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.6858 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6690 (p90)
  outliers start: 10
  outliers final: 1
  residues processed: 62
  average time/residue: 0.2280
  time to fit residues: 18.2538
Evaluate side-chains
  55 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0370
   overall best weight:    0.9062

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.129401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.091753 restraints weight = 9503.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.77
r_work: 0.2931 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6153  Z= 0.154
  Angle     :  0.600  11.949   8353  Z= 0.274
  Chirality :  0.044   0.291    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 11.157  65.253   1011
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  6.96 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.81 (0.34), residues: 692
  helix:  2.14 (0.29), residues: 355
  sheet:  1.83 (0.58), residues: 73
  loop : -0.28 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.006   0.001   HIS P  44 
 PHE   0.010   0.001   PHE A 286 
 TYR   0.015   0.001   TYR A 285 
 ARG   0.007   0.000   ARG A 671 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00804 (    4)
  link_NAG-ASN         : angle       3.62655 (   12)
  link_BETA1-4         : bond        0.00395 (    3)
  link_BETA1-4         : angle       1.71790 (    9)
  hydrogen bonds       : bond        0.04227 (  286)
  hydrogen bonds       : angle       3.85790 (  816)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.19548 (    2)
  covalent geometry    : bond        0.00363 ( 6145)
  covalent geometry    : angle       0.58175 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8389 (m-30)
REVERT: A  285 TYR cc_start: 0.8164 (t80) cc_final: 0.7963 (t80)
REVERT: A  619 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8506 (tm-30)
REVERT: A  663 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8519 (tp-100)
REVERT: A  680 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.6889 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6668 (p90)
  outliers start: 9
  outliers final: 3
  residues processed: 65
  average time/residue: 0.2272
  time to fit residues: 19.2009
Evaluate side-chains
  61 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0170
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3592 r_free = 0.3592 target = 0.125875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.087862 restraints weight = 9331.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.85
r_work: 0.2879 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6153  Z= 0.108
  Angle     :  0.568  12.558   8353  Z= 0.257
  Chirality :  0.040   0.278    905
  Planarity :  0.004   0.052   1034
  Dihedral  : 11.484  94.821   1011
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  7.91 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.12 (0.34), residues: 692
  helix:  2.47 (0.29), residues: 348
  sheet:  1.79 (0.58), residues: 73
  loop : -0.12 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.013   0.001   TYR A 285 
 ARG   0.005   0.000   ARG A 419 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01252 (    4)
  link_NAG-ASN         : angle       5.01519 (   12)
  link_BETA1-4         : bond        0.00439 (    3)
  link_BETA1-4         : angle       1.57375 (    9)
  hydrogen bonds       : bond        0.03674 (  286)
  hydrogen bonds       : angle       3.73340 (  816)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       0.10133 (    2)
  covalent geometry    : bond        0.00232 ( 6145)
  covalent geometry    : angle       0.53376 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8295 (t0)
REVERT: A  183 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8370 (m-30)
REVERT: A  417 ASP cc_start: 0.8218 (t0) cc_final: 0.7826 (t0)
REVERT: A  619 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8465 (tm-30)
REVERT: A  663 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8514 (tp-100)
REVERT: A  671 ARG cc_start: 0.9427 (tmm-80) cc_final: 0.8981 (ttp80)
REVERT: A  680 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.6876 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6569 (p90)
  outliers start: 6
  outliers final: 2
  residues processed: 64
  average time/residue: 0.2455
  time to fit residues: 20.9628
Evaluate side-chains
  62 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.123838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.085761 restraints weight = 9263.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.84
r_work: 0.2850 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2850
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6153  Z= 0.144
  Angle     :  0.565   9.990   8353  Z= 0.259
  Chirality :  0.041   0.210    905
  Planarity :  0.004   0.049   1034
  Dihedral  : 10.798  95.621   1011
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.86 %
    Favored  : 89.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.13 (0.34), residues: 692
  helix:  2.50 (0.29), residues: 348
  sheet:  1.76 (0.58), residues: 73
  loop : -0.14 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.008   0.001   PHE A 299 
 TYR   0.010   0.001   TYR A 285 
 ARG   0.004   0.000   ARG A 419 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00544 (    4)
  link_NAG-ASN         : angle       4.28587 (   12)
  link_BETA1-4         : bond        0.00323 (    3)
  link_BETA1-4         : angle       1.49560 (    9)
  hydrogen bonds       : bond        0.04010 (  286)
  hydrogen bonds       : angle       3.75432 (  816)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.10315 (    2)
  covalent geometry    : bond        0.00341 ( 6145)
  covalent geometry    : angle       0.53998 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8282 (t0)
REVERT: A  183 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8396 (m-30)
REVERT: A  236 TRP cc_start: 0.8668 (p-90) cc_final: 0.8458 (p-90)
REVERT: A  417 ASP cc_start: 0.8313 (t0) cc_final: 0.7889 (t0)
REVERT: A  619 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8470 (tm-30)
REVERT: A  663 GLN cc_start: 0.8914 (tp-100) cc_final: 0.7773 (tp-100)
REVERT: A  667 GLN cc_start: 0.9591 (mt0) cc_final: 0.9154 (mt0)
REVERT: A  680 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.6907 (ttt-90)
REVERT: P   94 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6626 (p90)
  outliers start: 8
  outliers final: 3
  residues processed: 65
  average time/residue: 0.2426
  time to fit residues: 20.5515
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.124213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.085818 restraints weight = 9426.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.87
r_work: 0.2850 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6153  Z= 0.134
  Angle     :  0.562   9.791   8353  Z= 0.259
  Chirality :  0.040   0.206    905
  Planarity :  0.004   0.049   1034
  Dihedral  : 10.824 106.960   1011
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.18 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.23 (0.34), residues: 692
  helix:  2.53 (0.29), residues: 348
  sheet:  1.92 (0.59), residues: 70
  loop : -0.00 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.015   0.001   TYR A 458 
 ARG   0.003   0.000   ARG A 419 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00939 (    4)
  link_NAG-ASN         : angle       4.83129 (   12)
  link_BETA1-4         : bond        0.00353 (    3)
  link_BETA1-4         : angle       1.41199 (    9)
  hydrogen bonds       : bond        0.03922 (  286)
  hydrogen bonds       : angle       3.72856 (  816)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.10119 (    2)
  covalent geometry    : bond        0.00310 ( 6145)
  covalent geometry    : angle       0.53055 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8292 (t0)
REVERT: A  183 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8367 (m-30)
REVERT: A  417 ASP cc_start: 0.8231 (t0) cc_final: 0.7844 (t0)
REVERT: A  619 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8467 (tm-30)
REVERT: A  663 GLN cc_start: 0.8923 (tp-100) cc_final: 0.7803 (tp-100)
REVERT: A  667 GLN cc_start: 0.9590 (mt0) cc_final: 0.9147 (mt0)
REVERT: A  680 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.6925 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8211 (tp40) cc_final: 0.8005 (tp40)
REVERT: P   94 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6654 (p90)
  outliers start: 7
  outliers final: 3
  residues processed: 66
  average time/residue: 0.2241
  time to fit residues: 19.3765
Evaluate side-chains
  68 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.122422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.084620 restraints weight = 9297.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.81
r_work: 0.2880 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6153  Z= 0.147
  Angle     :  0.563   9.820   8353  Z= 0.264
  Chirality :  0.040   0.184    905
  Planarity :  0.004   0.048   1034
  Dihedral  : 10.435 105.469   1011
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.49 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.19 (0.34), residues: 692
  helix:  2.50 (0.29), residues: 349
  sheet:  1.83 (0.57), residues: 76
  loop : -0.07 (0.42), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.008   0.001   PHE A 286 
 TYR   0.028   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00605 (    4)
  link_NAG-ASN         : angle       4.27728 (   12)
  link_BETA1-4         : bond        0.00351 (    3)
  link_BETA1-4         : angle       1.41039 (    9)
  hydrogen bonds       : bond        0.04102 (  286)
  hydrogen bonds       : angle       3.76016 (  816)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       0.11626 (    2)
  covalent geometry    : bond        0.00347 ( 6145)
  covalent geometry    : angle       0.53739 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8336 (t0)
REVERT: A  183 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8379 (m-30)
REVERT: A  417 ASP cc_start: 0.8365 (t0) cc_final: 0.7942 (t0)
REVERT: A  619 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: A  663 GLN cc_start: 0.8900 (tp-100) cc_final: 0.7741 (tp-100)
REVERT: A  667 GLN cc_start: 0.9584 (mt0) cc_final: 0.9138 (mt0)
REVERT: A  680 ARG cc_start: 0.7745 (mtp-110) cc_final: 0.6956 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8197 (tp40) cc_final: 0.7995 (tp40)
REVERT: P   94 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6652 (p90)
  outliers start: 7
  outliers final: 3
  residues processed: 67
  average time/residue: 0.2566
  time to fit residues: 21.9772
Evaluate side-chains
  67 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0570
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 65 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.125098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.086726 restraints weight = 9434.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.87
r_work: 0.2866 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6153  Z= 0.105
  Angle     :  0.543  10.571   8353  Z= 0.252
  Chirality :  0.039   0.147    905
  Planarity :  0.004   0.047   1034
  Dihedral  : 10.564 111.548   1011
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.97 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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:  2.26 (0.34), residues: 692
  helix:  2.57 (0.29), residues: 349
  sheet:  1.93 (0.59), residues: 70
  loop : -0.02 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.004   0.001   HIS P  44 
 PHE   0.006   0.001   PHE A 684 
 TYR   0.022   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00975 (    4)
  link_NAG-ASN         : angle       4.67280 (   12)
  link_BETA1-4         : bond        0.00388 (    3)
  link_BETA1-4         : angle       1.41717 (    9)
  hydrogen bonds       : bond        0.03649 (  286)
  hydrogen bonds       : angle       3.66865 (  816)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.03853 (    2)
  covalent geometry    : bond        0.00229 ( 6145)
  covalent geometry    : angle       0.51168 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8345 (t70)
REVERT: A  183 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8364 (m-30)
REVERT: A  619 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8478 (tm-30)
REVERT: A  663 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8390 (tp-100)
REVERT: A  680 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.6919 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8202 (tp40) cc_final: 0.7990 (tp40)
REVERT: P   94 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6682 (p90)
  outliers start: 6
  outliers final: 3
  residues processed: 67
  average time/residue: 0.2174
  time to fit residues: 18.9473
Evaluate side-chains
  65 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    0.2980
   chunk 57 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 44 optimal weight:    0.4980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3576 r_free = 0.3576 target = 0.124523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.086347 restraints weight = 9399.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.87
r_work: 0.2857 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6153  Z= 0.116
  Angle     :  0.547   9.481   8353  Z= 0.254
  Chirality :  0.039   0.155    905
  Planarity :  0.004   0.043   1034
  Dihedral  : 10.439 111.907   1011
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.13 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.27 (0.34), residues: 692
  helix:  2.55 (0.29), residues: 349
  sheet:  1.94 (0.59), residues: 70
  loop : -0.00 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.007   0.001   PHE A 684 
 TYR   0.017   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    4)
  link_NAG-ASN         : angle       3.95311 (   12)
  link_BETA1-4         : bond        0.00362 (    3)
  link_BETA1-4         : angle       1.39731 (    9)
  hydrogen bonds       : bond        0.03750 (  286)
  hydrogen bonds       : angle       3.67668 (  816)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.00610 (    2)
  covalent geometry    : bond        0.00266 ( 6145)
  covalent geometry    : angle       0.52469 ( 8330)

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

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

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1384 Ramachandran restraints generated.
    692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8343 (t0)
REVERT: A  183 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8376 (m-30)
REVERT: A  459 ASN cc_start: 0.7580 (t0) cc_final: 0.7349 (t0)
REVERT: A  619 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8504 (tm-30)
REVERT: A  663 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8475 (tp-100)
REVERT: A  680 ARG cc_start: 0.7822 (mtp-110) cc_final: 0.6924 (ttt-90)
REVERT: A  718 GLN cc_start: 0.8216 (tp40) cc_final: 0.8005 (tp40)
REVERT: P   94 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6691 (p90)
  outliers start: 6
  outliers final: 3
  residues processed: 63
  average time/residue: 0.2556
  time to fit residues: 21.1874
Evaluate side-chains
  66 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain P residue   94 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.123150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.085156 restraints weight = 9512.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.84
r_work: 0.2837 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6153  Z= 0.147
  Angle     :  0.565   8.602   8353  Z= 0.266
  Chirality :  0.040   0.154    905
  Planarity :  0.004   0.044   1034
  Dihedral  : 10.384 111.450   1011
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.81 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.19 (0.34), residues: 692
  helix:  2.51 (0.29), residues: 349
  sheet:  1.64 (0.57), residues: 78
  loop : -0.04 (0.42), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 160 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.022   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 419 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00279 (    4)
  link_NAG-ASN         : angle       3.86629 (   12)
  link_BETA1-4         : bond        0.00322 (    3)
  link_BETA1-4         : angle       1.39807 (    9)
  hydrogen bonds       : bond        0.04258 (  286)
  hydrogen bonds       : angle       3.74311 (  816)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.05763 (    2)
  covalent geometry    : bond        0.00349 ( 6145)
  covalent geometry    : angle       0.54484 ( 8330)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3189.89 seconds
wall clock time: 56 minutes 40.83 seconds (3400.83 seconds total)