Starting phenix.real_space_refine
on Sun Apr 27 08:09:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur5_42482/04_2025/8ur5_42482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur5_42482/04_2025/8ur5_42482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ur5_42482/04_2025/8ur5_42482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur5_42482/04_2025/8ur5_42482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur5_42482/04_2025/8ur5_42482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur5_42482/04_2025/8ur5_42482.cif"
  }
  resolution = 3.7
  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=   0.013 sd=   0.124
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      18      5.16       5
     C    3282      2.51       5
     N     858      2.21       5
     O     831      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4989
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1607
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 14, 'TRANS': 217}
          Unresolved non-hydrogen bonds: 238
          Unresolved non-hydrogen angles: 293
          Unresolved non-hydrogen dihedrals: 185
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 11, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 150
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 3.22, per 1000 atoms: 0.65
  Number of scatterers: 4989
  At special positions: 0
  Unit cell: (87.1141, 82.8298, 74.2612, 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      18     16.00
     O     831      8.00
     N     858      7.00
     C    3282      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A  94 " - pdb=" SG  CYS A 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 271 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  59 " - pdb=" SG  CYS B  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 107 " - pdb=" SG  CYS C 271 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 271 " distance=2.05

  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
    NAG-ASN
      " NAG A 501 " - " ASN A 163 "
      " NAG A 502 " - " ASN A 129 "
      " NAG A 503 " - " ASN A  58 "
      " NAG A 504 " - " ASN A  91 "
      " NAG B 501 " - " ASN B 163 "
      " NAG B 502 " - " ASN B 129 "
      " NAG B 503 " - " ASN B  58 "
      " NAG B 504 " - " ASN B  91 "
      " NAG C 501 " - " ASN C 163 "
      " NAG C 502 " - " ASN C 129 "
      " NAG C 503 " - " ASN C  58 "
      " NAG C 504 " - " ASN C  91 "
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 621.8 milliseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1284

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 15 sheets defined
      16.8% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.996A  pdb=" N   TRP A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'B' and resid 60 through 67
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 122 through 127
      removed outlier: 3.996A  pdb=" N   TRP B 127 " --> pdb=" O   LYS B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 275 through 283
    Processing helix  chain 'C' and resid 60 through 67
    Processing helix  chain 'C' and resid 101 through 106
    Processing helix  chain 'C' and resid 122 through 127
      removed outlier: 3.997A  pdb=" N   TRP C 127 " --> pdb=" O   LYS C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 275 through 283
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.625A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 141
    Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 169
    Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.624A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU C 175 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.624A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU C 175 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'C' and resid 164 through 169

    189 hydrogen bonds defined for protein.
    531 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: 1.65

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 753
        1.31 -     1.44: 1533
        1.44 -     1.57: 2841
        1.57 -     1.69: 9
        1.69 -     1.82: 18
  Bond restraints: 5154
  Sorted by residual:
  bond pdb=" C   ARG C 229 "
       pdb=" O   ARG C 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.048 1.24e-02 6.50e+03 1.53e+01
  bond pdb=" C   ARG B 229 "
       pdb=" O   ARG B 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.186  0.048 1.24e-02 6.50e+03 1.47e+01
  bond pdb=" C   ARG A 229 "
       pdb=" O   ARG A 229 "
    ideal  model  delta    sigma   weight residual
    1.234  1.187  0.047 1.24e-02 6.50e+03 1.45e+01
  bond pdb=" CA  ARG B 229 "
       pdb=" CB  ARG B 229 "
    ideal  model  delta    sigma   weight residual
    1.533  1.474  0.059 1.66e-02 3.63e+03 1.26e+01
  bond pdb=" CA  ARG A 229 "
       pdb=" CB  ARG A 229 "
    ideal  model  delta    sigma   weight residual
    1.533  1.474  0.059 1.66e-02 3.63e+03 1.26e+01
  ... (remaining 5149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 5765
        1.56 -     3.11: 1047
        3.11 -     4.67: 169
        4.67 -     6.23: 93
        6.23 -     7.79: 45
  Bond angle restraints: 7119
  Sorted by residual:
  angle pdb=" C   HIS B 184 "
        pdb=" N   PRO B 185 "
        pdb=" CA  PRO B 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.85   -7.19 7.30e-01 1.88e+00 9.71e+01
  angle pdb=" C   HIS A 184 "
        pdb=" N   PRO A 185 "
        pdb=" CA  PRO A 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.82   -7.16 7.30e-01 1.88e+00 9.63e+01
  angle pdb=" C   HIS C 184 "
        pdb=" N   PRO C 185 "
        pdb=" CA  PRO C 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.80   -7.14 7.30e-01 1.88e+00 9.56e+01
  angle pdb=" C   ASN A  88 "
        pdb=" N   PRO A  89 "
        pdb=" CA  PRO A  89 "
      ideal   model   delta    sigma   weight residual
     119.85  126.77   -6.92 1.01e+00 9.80e-01 4.70e+01
  angle pdb=" C   ASN B  88 "
        pdb=" N   PRO B  89 "
        pdb=" CA  PRO B  89 "
      ideal   model   delta    sigma   weight residual
     119.85  126.76   -6.91 1.01e+00 9.80e-01 4.68e+01
  ... (remaining 7114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.28: 2852
       12.28 -    24.55: 115
       24.55 -    36.83: 57
       36.83 -    49.10: 18
       49.10 -    61.38: 9
  Dihedral angle restraints: 3051
    sinusoidal: 1038
      harmonic: 2013
  Sorted by residual:
  dihedral pdb=" CB  CYS B  94 "
           pdb=" SG  CYS B  94 "
           pdb=" SG  CYS B 139 "
           pdb=" CB  CYS B 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.41  -37.41     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CB  CYS C  94 "
           pdb=" SG  CYS C  94 "
           pdb=" SG  CYS C 139 "
           pdb=" CB  CYS C 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.40  -37.40     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CB  CYS A  94 "
           pdb=" SG  CYS A  94 "
           pdb=" SG  CYS A 139 "
           pdb=" CB  CYS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.38  -37.38     1      1.00e+01 1.00e-02 1.97e+01
  ... (remaining 3048 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 529
       0.067 -    0.133: 230
       0.133 -    0.200: 27
       0.200 -    0.267: 33
       0.267 -    0.334: 15
  Chirality restraints: 834
  Sorted by residual:
  chirality pdb=" C2  NAG B 501 "
            pdb=" C1  NAG B 501 "
            pdb=" C3  NAG B 501 "
            pdb=" N2  NAG B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" C2  NAG C 501 "
            pdb=" C1  NAG C 501 "
            pdb=" C3  NAG C 501 "
            pdb=" N2  NAG C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" C2  NAG A 501 "
            pdb=" C1  NAG A 501 "
            pdb=" C3  NAG A 501 "
            pdb=" N2  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 831 not shown)

  Planarity restraints: 912
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  92 "   -0.014 2.00e-02 2.50e+03   2.89e-02 8.38e+00
        pdb=" C   GLY C  92 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY C  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR C  93 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  92 "   -0.014 2.00e-02 2.50e+03   2.89e-02 8.35e+00
        pdb=" C   GLY A  92 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR A  93 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  92 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.31e+00
        pdb=" C   GLY B  92 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLY B  92 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR B  93 "    0.017 2.00e-02 2.50e+03
  ... (remaining 909 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 2582
        2.99 -     3.47: 4265
        3.47 -     3.94: 7952
        3.94 -     4.42: 8647
        4.42 -     4.90: 14219
  Nonbonded interactions: 37665
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 163 "
            pdb=" N2  NAG B 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" OD1 ASN A 163 "
            pdb=" N2  NAG A 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" OD1 ASN C 163 "
            pdb=" N2  NAG C 501 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" O   ILE A 275 "
            pdb=" N   GLU A 278 "
     model   vdw
     2.541 3.120
  nonbonded pdb=" O   ILE B 275 "
            pdb=" N   GLU B 278 "
     model   vdw
     2.541 3.120
  ... (remaining 37660 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             0.280
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.280
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.760
  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: 0.7077
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      :  0.011   0.075   5175  Z= 0.662
  Angle     :  1.456   7.787   7173  Z= 1.010
  Chirality :  0.089   0.334    834
  Planarity :  0.005   0.029    900
  Dihedral  :  9.297  51.962   1740
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.35 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  3.42 %
    Favored  : 94.87 %
  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: -0.71 (0.29), residues: 690
  helix: -2.02 (0.42), residues: 117
  sheet:  2.31 (0.34), residues: 171
  loop : -1.32 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B  80 
 HIS   0.004   0.001   HIS C 130 
 PHE   0.010   0.002   PHE C 115 
 TYR   0.027   0.004   TYR B 195 
 ARG   0.002   0.001   ARG A 229 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05884 (   12)
  link_NAG-ASN         : angle       2.50903 (   36)
  hydrogen bonds       : bond        0.17864 (  168)
  hydrogen bonds       : angle       9.38373 (  531)
  SS BOND              : bond        0.01609 (    9)
  SS BOND              : angle       1.95828 (   18)
  covalent geometry    : bond        0.01061 ( 5154)
  covalent geometry    : angle       1.44711 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7726 (mtm110)
REVERT: A  230 ILE cc_start: 0.9278 (tt) cc_final: 0.9013 (tt)
REVERT: A  256 TYR cc_start: 0.8142 (m-80) cc_final: 0.7753 (m-10)
REVERT: B  229 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7723 (mtm110)
REVERT: B  256 TYR cc_start: 0.7999 (m-80) cc_final: 0.7524 (m-10)
REVERT: C  155 THR cc_start: 0.6919 (p) cc_final: 0.6688 (t)
REVERT: C  229 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7594 (mtm110)
REVERT: C  256 TYR cc_start: 0.7957 (m-80) cc_final: 0.7540 (m-10)
  outliers start: 6
  outliers final: 1
  residues processed: 170
  average time/residue: 0.2702
  time to fit residues: 56.3328
Evaluate side-chains
  106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain C residue  229 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0010
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.0790

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.166672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.133520 restraints weight = 8110.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132908 restraints weight = 6601.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.134486 restraints weight = 5394.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5175  Z= 0.166
  Angle     :  0.844  20.792   7173  Z= 0.396
  Chirality :  0.054   0.628    834
  Planarity :  0.005   0.022    900
  Dihedral  :  7.040  57.451   1012
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.33 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.80 %
    Favored  : 77.21 %
  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:  0.01 (0.31), residues: 690
  helix: -1.35 (0.48), residues: 117
  sheet:  1.92 (0.35), residues: 180
  loop : -0.47 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 153 
 HIS   0.004   0.001   HIS C 184 
 PHE   0.025   0.002   PHE C 147 
 TYR   0.016   0.002   TYR B  82 
 ARG   0.002   0.000   ARG C 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00915 (   12)
  link_NAG-ASN         : angle       6.26785 (   36)
  hydrogen bonds       : bond        0.04787 (  168)
  hydrogen bonds       : angle       7.30571 (  531)
  SS BOND              : bond        0.00461 (    9)
  SS BOND              : angle       3.11965 (   18)
  covalent geometry    : bond        0.00369 ( 5154)
  covalent geometry    : angle       0.70366 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8347 (t80) cc_final: 0.7998 (t80)
REVERT: A  224 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7498 (ttm170)
REVERT: A  229 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7776 (mtm110)
REVERT: A  237 LEU cc_start: 0.8853 (mt) cc_final: 0.8638 (mt)
REVERT: A  243 ILE cc_start: 0.8640 (tp) cc_final: 0.8376 (tt)
REVERT: A  256 TYR cc_start: 0.8625 (m-80) cc_final: 0.8137 (m-10)
REVERT: B  191 GLN cc_start: 0.7969 (tp40) cc_final: 0.7461 (tp40)
REVERT: B  229 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7842 (mtm110)
REVERT: B  256 TYR cc_start: 0.8500 (m-80) cc_final: 0.7971 (m-10)
REVERT: C  155 THR cc_start: 0.7332 (p) cc_final: 0.6799 (t)
REVERT: C  229 ARG cc_start: 0.8744 (ttm170) cc_final: 0.7754 (mtm110)
REVERT: C  256 TYR cc_start: 0.8333 (m-80) cc_final: 0.7957 (m-10)
  outliers start: 14
  outliers final: 7
  residues processed: 129
  average time/residue: 0.2218
  time to fit residues: 36.3783
Evaluate side-chains
  109 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0020
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.3594

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.164344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.129945 restraints weight = 8075.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130285 restraints weight = 8265.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.131179 restraints weight = 6807.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5175  Z= 0.164
  Angle     :  0.785  20.433   7173  Z= 0.366
  Chirality :  0.053   0.559    834
  Planarity :  0.004   0.025    900
  Dihedral  :  6.007  52.051   1003
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.48 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 19.94 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.31), residues: 690
  helix: -1.16 (0.49), residues: 117
  sheet:  1.34 (0.35), residues: 198
  loop : -0.38 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  64 
 HIS   0.004   0.001   HIS C 196 
 PHE   0.024   0.002   PHE C 118 
 TYR   0.019   0.002   TYR C  82 
 ARG   0.006   0.001   ARG B 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01557 (   12)
  link_NAG-ASN         : angle       5.75703 (   36)
  hydrogen bonds       : bond        0.04186 (  168)
  hydrogen bonds       : angle       6.70846 (  531)
  SS BOND              : bond        0.00619 (    9)
  SS BOND              : angle       2.69461 (   18)
  covalent geometry    : bond        0.00357 ( 5154)
  covalent geometry    : angle       0.65894 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  191 GLN cc_start: 0.8179 (tp40) cc_final: 0.7645 (tp40)
REVERT: A  229 ARG cc_start: 0.8278 (ttm170) cc_final: 0.7866 (mtm110)
REVERT: A  256 TYR cc_start: 0.8523 (m-80) cc_final: 0.7972 (m-10)
REVERT: B   66 LEU cc_start: 0.9154 (mp) cc_final: 0.8932 (mp)
REVERT: B  191 GLN cc_start: 0.8174 (tp40) cc_final: 0.7428 (tp40)
REVERT: B  229 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7442 (mtm110)
REVERT: B  256 TYR cc_start: 0.8481 (m-80) cc_final: 0.7401 (m-10)
REVERT: C   59 CYS cc_start: 0.5748 (p) cc_final: 0.5548 (p)
REVERT: C   80 TRP cc_start: 0.8885 (p90) cc_final: 0.8280 (p90)
REVERT: C  152 LEU cc_start: 0.7894 (mt) cc_final: 0.7597 (mt)
REVERT: C  229 ARG cc_start: 0.8675 (ttm170) cc_final: 0.7762 (mtm110)
REVERT: C  256 TYR cc_start: 0.8258 (m-80) cc_final: 0.7818 (m-10)
  outliers start: 18
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1918
  time to fit residues: 28.7603
Evaluate side-chains
  118 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0010
   chunk 13 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.163266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.129781 restraints weight = 8221.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.129734 restraints weight = 9201.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.130382 restraints weight = 7321.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5175  Z= 0.137
  Angle     :  0.751  18.472   7173  Z= 0.341
  Chirality :  0.052   0.556    834
  Planarity :  0.004   0.025    900
  Dihedral  :  5.774  47.264   1003
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.93 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 21.08 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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:  0.05 (0.32), residues: 690
  helix: -0.76 (0.52), residues: 114
  sheet:  1.13 (0.35), residues: 195
  loop : -0.23 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 180 
 HIS   0.005   0.001   HIS A 196 
 PHE   0.024   0.002   PHE C 118 
 TYR   0.018   0.002   TYR B 168 
 ARG   0.004   0.001   ARG B 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01310 (   12)
  link_NAG-ASN         : angle       5.88483 (   36)
  hydrogen bonds       : bond        0.03640 (  168)
  hydrogen bonds       : angle       6.39393 (  531)
  SS BOND              : bond        0.00416 (    9)
  SS BOND              : angle       2.23313 (   18)
  covalent geometry    : bond        0.00300 ( 5154)
  covalent geometry    : angle       0.61733 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A  191 GLN cc_start: 0.8414 (tp40) cc_final: 0.7799 (tp40)
REVERT: A  229 ARG cc_start: 0.8323 (ttm170) cc_final: 0.7596 (mtm110)
REVERT: A  232 TYR cc_start: 0.8409 (m-10) cc_final: 0.8189 (m-10)
REVERT: A  256 TYR cc_start: 0.8533 (m-80) cc_final: 0.7986 (m-10)
REVERT: B   66 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8905 (mp)
REVERT: B  191 GLN cc_start: 0.8365 (tp40) cc_final: 0.7587 (tp40)
REVERT: B  229 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.6870 (mtm110)
REVERT: C   80 TRP cc_start: 0.8805 (p90) cc_final: 0.8188 (p90)
REVERT: C  229 ARG cc_start: 0.8680 (ttm170) cc_final: 0.7724 (mtm110)
REVERT: C  256 TYR cc_start: 0.8295 (m-80) cc_final: 0.7874 (m-10)
  outliers start: 20
  outliers final: 10
  residues processed: 125
  average time/residue: 0.2146
  time to fit residues: 32.9913
Evaluate side-chains
  118 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0570
   overall best weight:    0.9902

-------------------------------------------------------------------------------
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 = 0.3873 r_free = 0.3873 target = 0.162741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.129412 restraints weight = 8229.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.129511 restraints weight = 8849.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130676 restraints weight = 6957.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5175  Z= 0.136
  Angle     :  0.722  17.940   7173  Z= 0.331
  Chirality :  0.050   0.500    834
  Planarity :  0.003   0.025    900
  Dihedral  :  5.747  43.963   1003
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.91 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 21.94 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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:  0.02 (0.32), residues: 690
  helix: -0.59 (0.53), residues: 114
  sheet:  0.96 (0.35), residues: 195
  loop : -0.23 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 180 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.023   0.002   PHE C 118 
 TYR   0.020   0.002   TYR B 168 
 ARG   0.005   0.001   ARG C 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01185 (   12)
  link_NAG-ASN         : angle       5.49212 (   36)
  hydrogen bonds       : bond        0.03509 (  168)
  hydrogen bonds       : angle       6.16582 (  531)
  SS BOND              : bond        0.00371 (    9)
  SS BOND              : angle       1.98149 (   18)
  covalent geometry    : bond        0.00295 ( 5154)
  covalent geometry    : angle       0.60268 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 ARG cc_start: 0.8329 (ttm170) cc_final: 0.7577 (mtm110)
REVERT: A  256 TYR cc_start: 0.8520 (m-80) cc_final: 0.8102 (m-10)
REVERT: B   66 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8879 (mp)
REVERT: B  106 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8423 (ttm-80)
REVERT: B  168 TYR cc_start: 0.8246 (t80) cc_final: 0.8012 (t80)
REVERT: B  191 GLN cc_start: 0.8476 (tp40) cc_final: 0.7672 (tp40)
REVERT: B  229 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.6795 (mtm110)
REVERT: C   80 TRP cc_start: 0.8738 (p90) cc_final: 0.8283 (p90)
REVERT: C  191 GLN cc_start: 0.8510 (tp40) cc_final: 0.7675 (tp40)
REVERT: C  229 ARG cc_start: 0.8572 (ttm170) cc_final: 0.7678 (mtm110)
REVERT: C  256 TYR cc_start: 0.8305 (m-80) cc_final: 0.7938 (m-10)
  outliers start: 23
  outliers final: 15
  residues processed: 121
  average time/residue: 0.2388
  time to fit residues: 36.0205
Evaluate side-chains
  117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    0.4980
   chunk 33 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   chunk 2 optimal weight:    0.0170
   chunk 26 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.6622

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.160100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.126400 restraints weight = 8187.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 79)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.122683 restraints weight = 8860.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.123306 restraints weight = 7817.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5175  Z= 0.173
  Angle     :  0.752  16.518   7173  Z= 0.348
  Chirality :  0.051   0.448    834
  Planarity :  0.004   0.037    900
  Dihedral  :  6.080  44.627   1003
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  3.91 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 21.65 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -0.10 (0.31), residues: 690
  helix: -0.76 (0.51), residues: 114
  sheet:  0.80 (0.35), residues: 195
  loop : -0.23 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 153 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.028   0.002   PHE C 118 
 TYR   0.023   0.002   TYR C 168 
 ARG   0.010   0.001   ARG A 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01105 (   12)
  link_NAG-ASN         : angle       5.33246 (   36)
  hydrogen bonds       : bond        0.03690 (  168)
  hydrogen bonds       : angle       6.20221 (  531)
  SS BOND              : bond        0.00345 (    9)
  SS BOND              : angle       2.32814 (   18)
  covalent geometry    : bond        0.00396 ( 5154)
  covalent geometry    : angle       0.64184 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  168 TYR cc_start: 0.8400 (t80) cc_final: 0.8099 (t80)
REVERT: B  191 GLN cc_start: 0.8444 (tp40) cc_final: 0.7625 (tp40)
REVERT: B  229 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6435 (mtm110)
REVERT: C   80 TRP cc_start: 0.8827 (p90) cc_final: 0.8320 (p90)
REVERT: C  229 ARG cc_start: 0.8687 (ttm170) cc_final: 0.7608 (mtm110)
REVERT: C  256 TYR cc_start: 0.8438 (m-80) cc_final: 0.8125 (m-10)
REVERT: C  274 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7793 (t-90)
  outliers start: 24
  outliers final: 16
  residues processed: 108
  average time/residue: 0.2851
  time to fit residues: 38.7262
Evaluate side-chains
  111 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  274 HIS
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0040
   chunk 21 optimal weight:    0.0070
   chunk 67 optimal weight:    9.9990
   overall best weight:    0.6612

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.162087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.127789 restraints weight = 8046.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.128096 restraints weight = 8179.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.129095 restraints weight = 6782.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5175  Z= 0.121
  Angle     :  0.763  20.485   7173  Z= 0.347
  Chirality :  0.048   0.297    834
  Planarity :  0.004   0.037    900
  Dihedral  :  5.931  50.035   1003
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  3.33 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 23.93 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -0.02 (0.32), residues: 690
  helix: -0.58 (0.52), residues: 114
  sheet:  0.85 (0.36), residues: 195
  loop : -0.21 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 180 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.027   0.002   PHE C 118 
 TYR   0.028   0.002   TYR C 168 
 ARG   0.009   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00552 (   12)
  link_NAG-ASN         : angle       5.31624 (   36)
  hydrogen bonds       : bond        0.03402 (  168)
  hydrogen bonds       : angle       6.08765 (  531)
  SS BOND              : bond        0.00330 (    9)
  SS BOND              : angle       3.18200 (   18)
  covalent geometry    : bond        0.00271 ( 5154)
  covalent geometry    : angle       0.64649 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8885 (OUTLIER) cc_final: 0.8475 (t-100)
REVERT: B  168 TYR cc_start: 0.8381 (t80) cc_final: 0.8038 (t80)
REVERT: B  191 GLN cc_start: 0.8611 (tp40) cc_final: 0.7711 (tp40)
REVERT: B  229 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6513 (mtm110)
REVERT: C   80 TRP cc_start: 0.8750 (p90) cc_final: 0.8311 (p90)
REVERT: C  172 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8616 (mttp)
REVERT: C  191 GLN cc_start: 0.8576 (tp40) cc_final: 0.7617 (tp40)
REVERT: C  229 ARG cc_start: 0.8561 (ttm170) cc_final: 0.7593 (mtm110)
REVERT: C  256 TYR cc_start: 0.8344 (m-80) cc_final: 0.8029 (m-10)
  outliers start: 20
  outliers final: 13
  residues processed: 106
  average time/residue: 0.2159
  time to fit residues: 28.8175
Evaluate side-chains
  108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.160930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.127068 restraints weight = 8065.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.128157 restraints weight = 8101.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.128798 restraints weight = 6451.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5175  Z= 0.132
  Angle     :  0.666   9.794   7173  Z= 0.314
  Chirality :  0.047   0.235    834
  Planarity :  0.004   0.032    900
  Dihedral  :  5.485  39.453   1003
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  3.77 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 25.36 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -0.10 (0.32), residues: 690
  helix: -0.63 (0.52), residues: 114
  sheet:  0.80 (0.36), residues: 195
  loop : -0.28 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 127 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.024   0.002   PHE C 118 
 TYR   0.031   0.002   TYR C 168 
 ARG   0.007   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00546 (   12)
  link_NAG-ASN         : angle       3.29871 (   36)
  hydrogen bonds       : bond        0.03469 (  168)
  hydrogen bonds       : angle       6.10689 (  531)
  SS BOND              : bond        0.00249 (    9)
  SS BOND              : angle       2.39871 (   18)
  covalent geometry    : bond        0.00303 ( 5154)
  covalent geometry    : angle       0.61449 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8908 (OUTLIER) cc_final: 0.8520 (t-100)
REVERT: B  168 TYR cc_start: 0.8460 (t80) cc_final: 0.7950 (t80)
REVERT: B  191 GLN cc_start: 0.8651 (tp40) cc_final: 0.7719 (tp40)
REVERT: B  229 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.6477 (mtm110)
REVERT: C   59 CYS cc_start: 0.5272 (p) cc_final: 0.5041 (p)
REVERT: C   80 TRP cc_start: 0.8776 (p90) cc_final: 0.8347 (p90)
REVERT: C  172 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8610 (mttp)
REVERT: C  191 GLN cc_start: 0.8617 (tp40) cc_final: 0.7668 (tp40)
REVERT: C  229 ARG cc_start: 0.8618 (ttm170) cc_final: 0.7583 (mtm110)
REVERT: C  256 TYR cc_start: 0.8374 (m-80) cc_final: 0.8024 (m-10)
REVERT: C  274 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7420 (t-90)
  outliers start: 19
  outliers final: 13
  residues processed: 106
  average time/residue: 0.2002
  time to fit residues: 26.7943
Evaluate side-chains
  105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 25 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.159299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.126595 restraints weight = 7871.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.126334 restraints weight = 9128.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.128324 restraints weight = 7285.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5175  Z= 0.168
  Angle     :  0.720  11.772   7173  Z= 0.336
  Chirality :  0.047   0.261    834
  Planarity :  0.004   0.042    900
  Dihedral  :  5.578  39.295   1003
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  3.91 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.92 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -0.22 (0.31), residues: 690
  helix: -0.63 (0.53), residues: 105
  sheet:  0.98 (0.38), residues: 180
  loop : -0.51 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 153 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.023   0.002   PHE C 118 
 TYR   0.030   0.002   TYR C 232 
 ARG   0.012   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00474 (   12)
  link_NAG-ASN         : angle       4.04104 (   36)
  hydrogen bonds       : bond        0.03716 (  168)
  hydrogen bonds       : angle       6.16282 (  531)
  SS BOND              : bond        0.00322 (    9)
  SS BOND              : angle       2.26215 (   18)
  covalent geometry    : bond        0.00397 ( 5154)
  covalent geometry    : angle       0.65330 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8895 (OUTLIER) cc_final: 0.8533 (t-100)
REVERT: B  168 TYR cc_start: 0.8461 (t80) cc_final: 0.7826 (t80)
REVERT: B  191 GLN cc_start: 0.8594 (tp40) cc_final: 0.7656 (tp40)
REVERT: B  229 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.6541 (mtm110)
REVERT: B  232 TYR cc_start: 0.8726 (m-80) cc_final: 0.8483 (m-10)
REVERT: C   80 TRP cc_start: 0.8795 (p90) cc_final: 0.8406 (p90)
REVERT: C  172 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8656 (mttp)
REVERT: C  229 ARG cc_start: 0.8608 (ttm170) cc_final: 0.7584 (mtm110)
REVERT: C  256 TYR cc_start: 0.8326 (m-80) cc_final: 0.8122 (m-10)
  outliers start: 16
  outliers final: 13
  residues processed: 98
  average time/residue: 0.2456
  time to fit residues: 30.2298
Evaluate side-chains
  104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0070
   chunk 50 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    1.7802

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.157425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.121891 restraints weight = 8436.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122807 restraints weight = 6887.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123237 restraints weight = 5734.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.5247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5175  Z= 0.172
  Angle     :  0.689  11.341   7173  Z= 0.331
  Chirality :  0.046   0.264    834
  Planarity :  0.004   0.048    900
  Dihedral  :  5.443  38.972   1003
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.35 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 27.64 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -0.39 (0.31), residues: 690
  helix: -0.88 (0.51), residues: 105
  sheet:  0.90 (0.38), residues: 180
  loop : -0.61 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.024   0.002   PHE B 118 
 TYR   0.031   0.002   TYR C 232 
 ARG   0.011   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00462 (   12)
  link_NAG-ASN         : angle       3.16777 (   36)
  hydrogen bonds       : bond        0.03785 (  168)
  hydrogen bonds       : angle       6.20143 (  531)
  SS BOND              : bond        0.00344 (    9)
  SS BOND              : angle       2.13895 (   18)
  covalent geometry    : bond        0.00406 ( 5154)
  covalent geometry    : angle       0.64538 ( 7119)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8908 (OUTLIER) cc_final: 0.8489 (t-100)
REVERT: A  229 ARG cc_start: 0.8453 (ttm170) cc_final: 0.7087 (mtm-85)
REVERT: B  168 TYR cc_start: 0.8646 (t80) cc_final: 0.7895 (t80)
REVERT: B  191 GLN cc_start: 0.8449 (tp40) cc_final: 0.7643 (tp40)
REVERT: B  229 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.6352 (mtm110)
REVERT: B  232 TYR cc_start: 0.8723 (m-80) cc_final: 0.8434 (m-10)
REVERT: C   80 TRP cc_start: 0.8866 (p90) cc_final: 0.8446 (p90)
REVERT: C  172 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8698 (mttp)
REVERT: C  229 ARG cc_start: 0.8728 (ttm170) cc_final: 0.7222 (mtm-85)
  outliers start: 15
  outliers final: 12
  residues processed: 100
  average time/residue: 0.2263
  time to fit residues: 28.7868
Evaluate side-chains
  102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TRP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   95 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0770
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.160378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.126062 restraints weight = 8346.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127091 restraints weight = 8514.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128428 restraints weight = 5958.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.5341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5175  Z= 0.109
  Angle     :  0.657  10.405   7173  Z= 0.308
  Chirality :  0.045   0.154    834
  Planarity :  0.004   0.044    900
  Dihedral  :  5.026  36.493   1003
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.06 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 28.77 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

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: -0.28 (0.31), residues: 690
  helix: -0.56 (0.53), residues: 105
  sheet:  0.95 (0.38), residues: 180
  loop : -0.58 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.005   0.001   HIS C 196 
 PHE   0.022   0.002   PHE B 118 
 TYR   0.028   0.002   TYR C 168 
 ARG   0.012   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00350 (   12)
  link_NAG-ASN         : angle       2.97981 (   36)
  hydrogen bonds       : bond        0.03397 (  168)
  hydrogen bonds       : angle       5.98950 (  531)
  SS BOND              : bond        0.00264 (    9)
  SS BOND              : angle       2.07189 (   18)
  covalent geometry    : bond        0.00248 ( 5154)
  covalent geometry    : angle       0.61543 ( 7119)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2641.97 seconds
wall clock time: 49 minutes 21.85 seconds (2961.85 seconds total)