Starting phenix.real_space_refine
on Thu Jul 24 13:05:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5m_13201/07_2025/7p5m_13201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5m_13201/07_2025/7p5m_13201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2025/7p5m_13201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2025/7p5m_13201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2025/7p5m_13201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2025/7p5m_13201.cif"
  }
  resolution = 3.92
  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=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4006      2.51       5
     N     976      2.21       5
     O    1176      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-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6204
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3018
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 9, 'TRANS': 384}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3018
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 9, 'TRANS': 384}
          Chain breaks: 1
    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: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      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: "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: 4.42, per 1000 atoms: 0.71
  Number of scatterers: 6204
  At special positions: 0
  Unit cell: (92.442, 70.308, 128.898, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1176      8.00
     N     976      7.00
     C    4006      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A 283 "
      " NAG A 602 " - " ASN A  31 "
      " NAG B 601 " - " ASN B 283 "
      " NAG B 602 " - " ASN B  31 "
      " NAG C   1 " - " ASN A 352 "
      " NAG D   1 " - " ASN A 129 "
      " NAG E   1 " - " ASN B 352 "
      " NAG F   1 " - " ASN B 129 "
  Time building additional restraints: 1.67
  Conformation dependent library (CDL) restraints added in 954.5 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      89.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 18
    Processing helix  chain 'A' and resid 38 through 70
      removed outlier: 3.660A  pdb=" N   ALA A  70 " --> pdb=" O   TYR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 159
      removed outlier: 4.199A  pdb=" N   LEU A 150 " --> pdb=" O   MET A 146 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 4.333A  pdb=" N   ALA A 163 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 187
    Processing helix  chain 'A' and resid 191 through 237
      removed outlier: 3.502A  pdb=" N   LEU A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 276
      removed outlier: 3.654A  pdb=" N   LEU A 242 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER A 244 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
    Processing helix  chain 'A' and resid 290 through 300
    Processing helix  chain 'A' and resid 308 through 337
      removed outlier: 3.971A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 341 through 365
    Processing helix  chain 'A' and resid 366 through 382
      removed outlier: 4.426A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 414
      removed outlier: 3.682A  pdb=" N   GLN A 387 " --> pdb=" O   TYR A 383 " (cutoff:3.500A)
      Proline residue:  A 411  - end of helix
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 38 through 70
      removed outlier: 3.646A  pdb=" N   ALA B  70 " --> pdb=" O   TYR B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 159
      removed outlier: 4.245A  pdb=" N   LEU B 150 " --> pdb=" O   MET B 146 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 4.284A  pdb=" N   ALA B 163 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 187
    Processing helix  chain 'B' and resid 191 through 237
      removed outlier: 3.611A  pdb=" N   LEU B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 276
      removed outlier: 3.739A  pdb=" N   LEU B 242 " --> pdb=" O   SER B 238 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER B 244 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
    Processing helix  chain 'B' and resid 290 through 300
    Processing helix  chain 'B' and resid 308 through 337
      removed outlier: 4.127A  pdb=" N   VAL B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      Proline residue:  B 335  - end of helix
    Processing helix  chain 'B' and resid 341 through 365
    Processing helix  chain 'B' and resid 366 through 383
      removed outlier: 4.418A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 409
      removed outlier: 3.543A  pdb=" N   GLN B 387 " --> pdb=" O   TYR B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 414

    562 hydrogen bonds defined for protein.
    1680 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: 1.95

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1918
        1.34 -     1.46: 1290
        1.46 -     1.58: 3062
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6332
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.01e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  ... (remaining 6327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 8391
        1.59 -     3.19: 201
        3.19 -     4.78: 25
        4.78 -     6.37: 8
        6.37 -     7.97: 5
  Bond angle restraints: 8630
  Sorted by residual:
  angle pdb=" C   LEU B 282 "
        pdb=" N   ASN B 283 "
        pdb=" CA  ASN B 283 "
      ideal   model   delta    sigma   weight residual
     122.65  116.56    6.09 1.60e+00 3.91e-01 1.45e+01
  angle pdb=" C   ASP B 166 "
        pdb=" N   TYR B 167 "
        pdb=" CA  TYR B 167 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" C   ASP A 166 "
        pdb=" N   TYR A 167 "
        pdb=" CA  TYR A 167 "
      ideal   model   delta    sigma   weight residual
     121.54  127.82   -6.28 1.91e+00 2.74e-01 1.08e+01
  angle pdb=" C   LEU A 282 "
        pdb=" N   ASN A 283 "
        pdb=" CA  ASN A 283 "
      ideal   model   delta    sigma   weight residual
     122.38  116.47    5.91 1.81e+00 3.05e-01 1.07e+01
  angle pdb=" N   VAL B  23 "
        pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     113.71  110.95    2.76 9.50e-01 1.11e+00 8.42e+00
  ... (remaining 8625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.30: 3538
       21.30 -    42.59: 249
       42.59 -    63.89: 39
       63.89 -    85.18: 6
       85.18 -   106.48: 16
  Dihedral angle restraints: 3848
    sinusoidal: 1562
      harmonic: 2286
  Sorted by residual:
  dihedral pdb=" CB  CYS A 300 "
           pdb=" SG  CYS A 300 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.58   31.42     1      1.00e+01 1.00e-02 1.41e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   68.63  106.48     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" C5  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -52.46  106.24     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 3845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 901
       0.051 -    0.102: 148
       0.102 -    0.152: 11
       0.152 -    0.203: 4
       0.203 -    0.254: 2
  Chirality restraints: 1066
  Sorted by residual:
  chirality pdb=" CA  ASN A 283 "
            pdb=" N   ASN A 283 "
            pdb=" C   ASN A 283 "
            pdb=" CB  ASN A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 129 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A 283 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1063 not shown)

  Planarity restraints: 1058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 283 "    0.001 2.00e-02 2.50e+03   3.05e-02 1.16e+01
        pdb=" CG  ASN A 283 "    0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 283 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 283 "    0.035 2.00e-02 2.50e+03
        pdb=" C1  NAG A 601 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 167 "    0.017 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   TYR B 167 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   TYR B 167 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU B 168 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 167 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   TYR A 167 "    0.055 2.00e-02 2.50e+03
        pdb=" O   TYR A 167 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 168 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1055 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 823
        2.75 -     3.29: 6592
        3.29 -     3.82: 10801
        3.82 -     4.36: 11266
        4.36 -     4.90: 20145
  Nonbonded interactions: 49627
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   LEU A 154 "
            pdb=" OG  SER A 158 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU A 151 "
            pdb=" NE2 GLN A 175 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN B  31 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD2 ASP A  38 "
            pdb=" OG  SER A  40 "
     model   vdw
     2.259 3.040
  ... (remaining 49622 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 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.430
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
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      :  0.003   0.033   6348  Z= 0.168
  Angle     :  0.631   8.747   8674  Z= 0.304
  Chirality :  0.039   0.254   1066
  Planarity :  0.004   0.052   1050
  Dihedral  : 16.498 106.479   2368
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  3.52 (0.30), residues: 780
  helix:  2.66 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.33 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 414 
 HIS   0.003   0.001   HIS B  18 
 PHE   0.020   0.001   PHE B 395 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.004   0.000   ARG B  26 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00613 (    8)
  link_NAG-ASN         : angle       2.89512 (   24)
  link_BETA1-4         : bond        0.01570 (    4)
  link_BETA1-4         : angle       3.77055 (   12)
  hydrogen bonds       : bond        0.11116 (  562)
  hydrogen bonds       : angle       4.77758 ( 1680)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       0.63626 (    8)
  covalent geometry    : bond        0.00344 ( 6332)
  covalent geometry    : angle       0.59690 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7340 (t0) cc_final: 0.7015 (t0)
REVERT: A  406 MET cc_start: 0.8207 (tmm) cc_final: 0.7957 (tmm)
REVERT: B  127 ASP cc_start: 0.7753 (t0) cc_final: 0.7064 (t0)
REVERT: B  166 ASP cc_start: 0.7517 (p0) cc_final: 0.7070 (m-30)
REVERT: B  210 TYR cc_start: 0.6851 (t80) cc_final: 0.6566 (t80)
REVERT: B  341 GLU cc_start: 0.8057 (pp20) cc_final: 0.7557 (pp20)
REVERT: B  406 MET cc_start: 0.8378 (tmm) cc_final: 0.8087 (tmm)
REVERT: B  412 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7477 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1460
  time to fit residues: 40.8765
Evaluate side-chains
  188 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0970
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.177849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.152203 restraints weight = 8624.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.156254 restraints weight = 4995.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.158792 restraints weight = 3429.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6348  Z= 0.140
  Angle     :  0.607   7.660   8674  Z= 0.296
  Chirality :  0.039   0.196   1066
  Planarity :  0.004   0.053   1050
  Dihedral  : 11.141  73.663   1090
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.54 %
    Favored  : 85.93 %
  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:  3.62 (0.29), residues: 780
  helix:  2.73 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.34 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.013   0.001   PHE A  47 
 TYR   0.011   0.001   TYR B 167 
 ARG   0.004   0.001   ARG B  26 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00589 (    8)
  link_NAG-ASN         : angle       1.47183 (   24)
  link_BETA1-4         : bond        0.01341 (    4)
  link_BETA1-4         : angle       3.38344 (   12)
  hydrogen bonds       : bond        0.04665 (  562)
  hydrogen bonds       : angle       4.13206 ( 1680)
  SS BOND              : bond        0.00772 (    4)
  SS BOND              : angle       1.53562 (    8)
  covalent geometry    : bond        0.00284 ( 6332)
  covalent geometry    : angle       0.58830 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 212
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7399 (t0) cc_final: 0.6895 (t0)
REVERT: A  406 MET cc_start: 0.8243 (tmm) cc_final: 0.8037 (tmm)
REVERT: B  127 ASP cc_start: 0.7822 (t0) cc_final: 0.7152 (t0)
REVERT: B  166 ASP cc_start: 0.7644 (p0) cc_final: 0.7070 (p0)
REVERT: B  210 TYR cc_start: 0.6816 (t80) cc_final: 0.6396 (t80)
REVERT: B  325 GLN cc_start: 0.7437 (mp10) cc_final: 0.7166 (mp10)
REVERT: B  341 GLU cc_start: 0.8019 (pp20) cc_final: 0.7482 (pp20)
REVERT: B  406 MET cc_start: 0.8503 (tmm) cc_final: 0.8206 (tmm)
REVERT: B  412 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7264 (ttm170)
  outliers start: 10
  outliers final: 7
  residues processed: 214
  average time/residue: 0.1528
  time to fit residues: 44.7654
Evaluate side-chains
  204 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 197
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 70 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.178263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.153115 restraints weight = 8778.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.156976 restraints weight = 5161.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.159163 restraints weight = 3586.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6348  Z= 0.132
  Angle     :  0.601   9.789   8674  Z= 0.287
  Chirality :  0.038   0.178   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  7.689  55.956   1090
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.28 %
    Favored  : 80.58 %
  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:  3.66 (0.29), residues: 780
  helix:  2.78 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.19 (0.58), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  13 
 HIS   0.002   0.000   HIS B  18 
 PHE   0.021   0.001   PHE A  47 
 TYR   0.010   0.001   TYR B 167 
 ARG   0.004   0.000   ARG B 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00565 (    8)
  link_NAG-ASN         : angle       1.29729 (   24)
  link_BETA1-4         : bond        0.01505 (    4)
  link_BETA1-4         : angle       3.69433 (   12)
  hydrogen bonds       : bond        0.04264 (  562)
  hydrogen bonds       : angle       3.96410 ( 1680)
  SS BOND              : bond        0.00685 (    4)
  SS BOND              : angle       1.50174 (    8)
  covalent geometry    : bond        0.00267 ( 6332)
  covalent geometry    : angle       0.58063 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 221
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7455 (t0) cc_final: 0.6715 (t0)
REVERT: A  209 GLU cc_start: 0.7705 (tp30) cc_final: 0.7472 (tp30)
REVERT: A  412 ARG cc_start: 0.7833 (mtt180) cc_final: 0.7194 (ttm170)
REVERT: B  127 ASP cc_start: 0.7843 (t0) cc_final: 0.7130 (t0)
REVERT: B  166 ASP cc_start: 0.8011 (p0) cc_final: 0.7230 (m-30)
REVERT: B  210 TYR cc_start: 0.6787 (t80) cc_final: 0.6466 (t80)
REVERT: B  325 GLN cc_start: 0.7591 (mp10) cc_final: 0.7343 (mp10)
REVERT: B  341 GLU cc_start: 0.8108 (pp20) cc_final: 0.7543 (pp20)
REVERT: B  406 MET cc_start: 0.8598 (tmm) cc_final: 0.8264 (tmm)
REVERT: B  412 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7187 (ttm170)
  outliers start: 14
  outliers final: 11
  residues processed: 223
  average time/residue: 0.1409
  time to fit residues: 42.9498
Evaluate side-chains
  219 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 208
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0470
   chunk 74 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.175775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.150273 restraints weight = 8828.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.154328 restraints weight = 5079.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.156934 restraints weight = 3465.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6348  Z= 0.132
  Angle     :  0.600   8.397   8674  Z= 0.288
  Chirality :  0.038   0.173   1066
  Planarity :  0.004   0.058   1050
  Dihedral  :  6.290  51.578   1090
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 22.02 %
    Favored  : 76.45 %
  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:  3.73 (0.29), residues: 780
  helix:  2.85 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.04 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.021   0.001   PHE B 173 
 TYR   0.010   0.001   TYR A 374 
 ARG   0.002   0.000   ARG B 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00537 (    8)
  link_NAG-ASN         : angle       1.30003 (   24)
  link_BETA1-4         : bond        0.01615 (    4)
  link_BETA1-4         : angle       4.17124 (   12)
  hydrogen bonds       : bond        0.04147 (  562)
  hydrogen bonds       : angle       3.86909 ( 1680)
  SS BOND              : bond        0.00483 (    4)
  SS BOND              : angle       1.78626 (    8)
  covalent geometry    : bond        0.00275 ( 6332)
  covalent geometry    : angle       0.57437 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 220
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7365 (t0) cc_final: 0.6604 (t0)
REVERT: A  166 ASP cc_start: 0.7960 (p0) cc_final: 0.7433 (p0)
REVERT: A  412 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7231 (ttm170)
REVERT: B  127 ASP cc_start: 0.7749 (t0) cc_final: 0.7072 (t0)
REVERT: B  166 ASP cc_start: 0.7966 (p0) cc_final: 0.7449 (p0)
REVERT: B  210 TYR cc_start: 0.6886 (t80) cc_final: 0.6519 (t80)
REVERT: B  341 GLU cc_start: 0.7848 (pp20) cc_final: 0.7440 (pp20)
REVERT: B  406 MET cc_start: 0.8649 (tmm) cc_final: 0.8315 (tmm)
REVERT: B  412 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7187 (ttm170)
  outliers start: 10
  outliers final: 8
  residues processed: 222
  average time/residue: 0.1538
  time to fit residues: 46.8665
Evaluate side-chains
  217 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 209
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 40 optimal weight:    0.1980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.177785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.152953 restraints weight = 8747.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.156626 restraints weight = 5199.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.159057 restraints weight = 3651.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6348  Z= 0.132
  Angle     :  0.604   8.371   8674  Z= 0.289
  Chirality :  0.038   0.265   1066
  Planarity :  0.004   0.058   1050
  Dihedral  :  5.868  45.578   1090
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 23.09 %
    Favored  : 74.92 %
  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:  3.78 (0.29), residues: 780
  helix:  2.89 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.11 (0.57), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.023   0.002   PHE B 173 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00566 (    8)
  link_NAG-ASN         : angle       1.33385 (   24)
  link_BETA1-4         : bond        0.01554 (    4)
  link_BETA1-4         : angle       4.18965 (   12)
  hydrogen bonds       : bond        0.04032 (  562)
  hydrogen bonds       : angle       3.82031 ( 1680)
  SS BOND              : bond        0.00576 (    4)
  SS BOND              : angle       1.68536 (    8)
  covalent geometry    : bond        0.00277 ( 6332)
  covalent geometry    : angle       0.57806 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 215
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7557 (t0) cc_final: 0.6892 (t70)
REVERT: A  166 ASP cc_start: 0.8033 (p0) cc_final: 0.7382 (p0)
REVERT: A  167 TYR cc_start: 0.7853 (m-10) cc_final: 0.7547 (m-10)
REVERT: A  412 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7237 (ttm170)
REVERT: B  166 ASP cc_start: 0.8115 (p0) cc_final: 0.7736 (p0)
REVERT: B  210 TYR cc_start: 0.6953 (t80) cc_final: 0.6648 (t80)
REVERT: B  325 GLN cc_start: 0.7763 (mp10) cc_final: 0.7157 (mp10)
REVERT: B  341 GLU cc_start: 0.7958 (pp20) cc_final: 0.7511 (pp20)
REVERT: B  366 ASP cc_start: 0.8904 (t0) cc_final: 0.8654 (t70)
REVERT: B  406 MET cc_start: 0.8683 (tmm) cc_final: 0.8329 (tmm)
  outliers start: 13
  outliers final: 12
  residues processed: 217
  average time/residue: 0.1438
  time to fit residues: 42.8649
Evaluate side-chains
  225 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 213
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 52 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.176923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.152046 restraints weight = 8690.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.155675 restraints weight = 5204.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.158113 restraints weight = 3668.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6348  Z= 0.135
  Angle     :  0.615   8.823   8674  Z= 0.293
  Chirality :  0.038   0.253   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.526  39.986   1090
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.55 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.85 (0.29), residues: 780
  helix:  2.93 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop : -0.02 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.023   0.002   PHE B 173 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00544 (    8)
  link_NAG-ASN         : angle       1.35612 (   24)
  link_BETA1-4         : bond        0.01480 (    4)
  link_BETA1-4         : angle       4.19802 (   12)
  hydrogen bonds       : bond        0.04039 (  562)
  hydrogen bonds       : angle       3.78871 ( 1680)
  SS BOND              : bond        0.00617 (    4)
  SS BOND              : angle       1.80460 (    8)
  covalent geometry    : bond        0.00287 ( 6332)
  covalent geometry    : angle       0.58928 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 219
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7551 (t0) cc_final: 0.6875 (t70)
REVERT: A  166 ASP cc_start: 0.8044 (p0) cc_final: 0.7594 (p0)
REVERT: A  412 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7134 (ttm170)
REVERT: B  166 ASP cc_start: 0.7792 (p0) cc_final: 0.7409 (p0)
REVERT: B  210 TYR cc_start: 0.6918 (t80) cc_final: 0.6623 (t80)
REVERT: B  325 GLN cc_start: 0.7787 (mp10) cc_final: 0.7175 (mp10)
REVERT: B  337 PHE cc_start: 0.6703 (m-10) cc_final: 0.6432 (m-10)
REVERT: B  341 GLU cc_start: 0.7897 (pp20) cc_final: 0.7489 (pp20)
REVERT: B  366 ASP cc_start: 0.8946 (t0) cc_final: 0.8699 (t70)
REVERT: B  406 MET cc_start: 0.8639 (tmm) cc_final: 0.8266 (tmm)
  outliers start: 16
  outliers final: 13
  residues processed: 224
  average time/residue: 0.1490
  time to fit residues: 46.2078
Evaluate side-chains
  229 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 216
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 42 optimal weight:    0.3980
   chunk 76 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3949 r_free = 0.3949 target = 0.177017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.152497 restraints weight = 8731.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.156219 restraints weight = 5178.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.158598 restraints weight = 3614.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6348  Z= 0.127
  Angle     :  0.612   8.252   8674  Z= 0.290
  Chirality :  0.037   0.244   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.351  38.648   1090
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 25.69 %
    Favored  : 72.48 %
  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:  3.97 (0.29), residues: 780
  helix:  3.00 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.08 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  22 
 PHE   0.018   0.001   PHE A  47 
 TYR   0.007   0.001   TYR A 374 
 ARG   0.007   0.000   ARG B 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00557 (    8)
  link_NAG-ASN         : angle       1.34090 (   24)
  link_BETA1-4         : bond        0.01469 (    4)
  link_BETA1-4         : angle       4.13211 (   12)
  hydrogen bonds       : bond        0.03963 (  562)
  hydrogen bonds       : angle       3.74972 ( 1680)
  SS BOND              : bond        0.00484 (    4)
  SS BOND              : angle       1.75948 (    8)
  covalent geometry    : bond        0.00268 ( 6332)
  covalent geometry    : angle       0.58760 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 221
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7543 (t0) cc_final: 0.6897 (t70)
REVERT: A  378 LEU cc_start: 0.8175 (mt) cc_final: 0.7867 (mp)
REVERT: A  412 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7126 (ttm170)
REVERT: B  166 ASP cc_start: 0.7852 (p0) cc_final: 0.6952 (p0)
REVERT: B  210 TYR cc_start: 0.6907 (t80) cc_final: 0.6600 (t80)
REVERT: B  337 PHE cc_start: 0.6832 (m-10) cc_final: 0.6539 (m-10)
REVERT: B  341 GLU cc_start: 0.7794 (pp20) cc_final: 0.7380 (pp20)
REVERT: B  366 ASP cc_start: 0.8948 (t0) cc_final: 0.8694 (t70)
  outliers start: 12
  outliers final: 12
  residues processed: 225
  average time/residue: 0.1409
  time to fit residues: 43.3409
Evaluate side-chains
  226 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 214
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.176345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.151548 restraints weight = 8703.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.155464 restraints weight = 5070.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.157989 restraints weight = 3490.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6348  Z= 0.135
  Angle     :  0.636   8.543   8674  Z= 0.301
  Chirality :  0.038   0.240   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.256  38.462   1090
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 25.69 %
    Favored  : 71.87 %
  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:  3.97 (0.29), residues: 780
  helix:  2.98 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.21 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.023   0.001   PHE B 173 
 TYR   0.007   0.001   TYR B 167 
 ARG   0.010   0.001   ARG B 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00538 (    8)
  link_NAG-ASN         : angle       1.35347 (   24)
  link_BETA1-4         : bond        0.01411 (    4)
  link_BETA1-4         : angle       4.11510 (   12)
  hydrogen bonds       : bond        0.03967 (  562)
  hydrogen bonds       : angle       3.76883 ( 1680)
  SS BOND              : bond        0.00520 (    4)
  SS BOND              : angle       1.83794 (    8)
  covalent geometry    : bond        0.00289 ( 6332)
  covalent geometry    : angle       0.61238 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7551 (t0) cc_final: 0.6882 (t70)
REVERT: A  166 ASP cc_start: 0.7953 (p0) cc_final: 0.7590 (p0)
REVERT: A  412 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7194 (ttm170)
REVERT: B  166 ASP cc_start: 0.7849 (p0) cc_final: 0.7485 (p0)
REVERT: B  210 TYR cc_start: 0.6880 (t80) cc_final: 0.6609 (t80)
REVERT: B  295 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7824 (mtp-110)
REVERT: B  337 PHE cc_start: 0.6821 (m-10) cc_final: 0.6581 (m-10)
REVERT: B  341 GLU cc_start: 0.7734 (pp20) cc_final: 0.7384 (pp20)
  outliers start: 16
  outliers final: 14
  residues processed: 221
  average time/residue: 0.1353
  time to fit residues: 41.3719
Evaluate side-chains
  224 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 210
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.175839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.151025 restraints weight = 8744.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.154875 restraints weight = 5122.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157387 restraints weight = 3543.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6348  Z= 0.141
  Angle     :  0.640   8.268   8674  Z= 0.303
  Chirality :  0.038   0.243   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.193  38.502   1090
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 25.84 %
    Favored  : 71.71 %
  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:  3.91 (0.29), residues: 780
  helix:  2.93 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.25 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 257 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.018   0.002   PHE B  47 
 TYR   0.010   0.001   TYR B 374 
 ARG   0.009   0.001   ARG B 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00552 (    8)
  link_NAG-ASN         : angle       1.37562 (   24)
  link_BETA1-4         : bond        0.01409 (    4)
  link_BETA1-4         : angle       4.11742 (   12)
  hydrogen bonds       : bond        0.04001 (  562)
  hydrogen bonds       : angle       3.79443 ( 1680)
  SS BOND              : bond        0.00539 (    4)
  SS BOND              : angle       1.98990 (    8)
  covalent geometry    : bond        0.00306 ( 6332)
  covalent geometry    : angle       0.61629 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 214
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7560 (t0) cc_final: 0.6903 (t70)
REVERT: A  166 ASP cc_start: 0.7974 (p0) cc_final: 0.7158 (p0)
REVERT: A  412 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7198 (ttm170)
REVERT: B  166 ASP cc_start: 0.7888 (p0) cc_final: 0.7602 (p0)
REVERT: B  210 TYR cc_start: 0.6858 (t80) cc_final: 0.6568 (t80)
REVERT: B  337 PHE cc_start: 0.6767 (m-10) cc_final: 0.6540 (m-10)
REVERT: B  341 GLU cc_start: 0.7775 (pp20) cc_final: 0.7400 (pp20)
  outliers start: 16
  outliers final: 16
  residues processed: 222
  average time/residue: 0.1378
  time to fit residues: 42.3244
Evaluate side-chains
  228 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 212
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.174733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.150320 restraints weight = 8866.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.154015 restraints weight = 5230.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.156243 restraints weight = 3642.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6348  Z= 0.145
  Angle     :  0.659   8.231   8674  Z= 0.312
  Chirality :  0.038   0.246   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.155  38.755   1090
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.38 %
    Favored  : 72.02 %
  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:  3.89 (0.29), residues: 780
  helix:  2.91 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.30 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 257 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.019   0.001   PHE A  47 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.008   0.001   ARG B 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00539 (    8)
  link_NAG-ASN         : angle       1.39556 (   24)
  link_BETA1-4         : bond        0.01384 (    4)
  link_BETA1-4         : angle       4.11187 (   12)
  hydrogen bonds       : bond        0.04065 (  562)
  hydrogen bonds       : angle       3.79900 ( 1680)
  SS BOND              : bond        0.00535 (    4)
  SS BOND              : angle       2.06327 (    8)
  covalent geometry    : bond        0.00318 ( 6332)
  covalent geometry    : angle       0.63514 ( 8630)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 213
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7575 (t0) cc_final: 0.6917 (t70)
REVERT: A  166 ASP cc_start: 0.8058 (p0) cc_final: 0.7538 (p0)
REVERT: A  412 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7183 (ttm170)
REVERT: B  166 ASP cc_start: 0.7930 (p0) cc_final: 0.7638 (p0)
REVERT: B  210 TYR cc_start: 0.6906 (t80) cc_final: 0.6613 (t80)
REVERT: B  337 PHE cc_start: 0.6808 (m-10) cc_final: 0.6591 (m-10)
REVERT: B  341 GLU cc_start: 0.7776 (pp20) cc_final: 0.7402 (pp20)
  outliers start: 17
  outliers final: 16
  residues processed: 221
  average time/residue: 0.1316
  time to fit residues: 40.7690
Evaluate side-chains
  231 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 59 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0010
   chunk 33 optimal weight:    0.9980
   chunk 55 optimal weight:    0.3980
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.4186

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.177422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.152968 restraints weight = 8923.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.156739 restraints weight = 5269.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.159004 restraints weight = 3662.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6348  Z= 0.131
  Angle     :  0.664  11.678   8674  Z= 0.311
  Chirality :  0.038   0.233   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.080  38.275   1090
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 25.84 %
    Favored  : 71.71 %
  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:  3.95 (0.29), residues: 780
  helix:  2.95 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.35 (0.58), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.020   0.001   PHE A  47 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.009   0.001   ARG A 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00578 (    8)
  link_NAG-ASN         : angle       1.36123 (   24)
  link_BETA1-4         : bond        0.01430 (    4)
  link_BETA1-4         : angle       4.04769 (   12)
  hydrogen bonds       : bond        0.03955 (  562)
  hydrogen bonds       : angle       3.77132 ( 1680)
  SS BOND              : bond        0.00429 (    4)
  SS BOND              : angle       1.75099 (    8)
  covalent geometry    : bond        0.00280 ( 6332)
  covalent geometry    : angle       0.64258 ( 8630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2130.57 seconds
wall clock time: 38 minutes 7.17 seconds (2287.17 seconds total)