Starting phenix.real_space_refine
on Sat May 10 04:43:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur5_42482/05_2025/8ur5_42482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur5_42482/05_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_42482/05_2025/8ur5_42482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur5_42482/05_2025/8ur5_42482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur5_42482/05_2025/8ur5_42482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur5_42482/05_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.15, per 1000 atoms: 0.63
  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: 1.23
  Conformation dependent library (CDL) restraints added in 666.2 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: 0.70
  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: 1.30

  Time building geometry restraints manager: 1.47 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: 0.04
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:             0.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.560
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.290
-------------------------------------------------------------------------------
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  : 0.576 
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: 0.2189
  time to fit residues: 45.2883
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  : 0.542 
-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.133770 restraints weight = 8110.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.133499 restraints weight = 6462.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.134893 restraints weight = 5349.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
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  : 0.580 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8279 (t80) cc_final: 0.7939 (t80)
REVERT: A  224 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7516 (ttm170)
REVERT: A  229 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7740 (mtm110)
REVERT: A  237 LEU cc_start: 0.8841 (mt) cc_final: 0.8615 (mt)
REVERT: A  243 ILE cc_start: 0.8628 (tp) cc_final: 0.8355 (tt)
REVERT: A  256 TYR cc_start: 0.8693 (m-80) cc_final: 0.8201 (m-10)
REVERT: B  191 GLN cc_start: 0.7955 (tp40) cc_final: 0.7451 (tp40)
REVERT: B  229 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7815 (mtm110)
REVERT: B  256 TYR cc_start: 0.8565 (m-80) cc_final: 0.8035 (m-10)
REVERT: C  155 THR cc_start: 0.7318 (p) cc_final: 0.6781 (t)
REVERT: C  229 ARG cc_start: 0.8772 (ttm170) cc_final: 0.7692 (mtm110)
REVERT: C  232 TYR cc_start: 0.8562 (m-80) cc_final: 0.8344 (m-10)
REVERT: C  256 TYR cc_start: 0.8397 (m-80) cc_final: 0.8051 (m-10)
  outliers start: 14
  outliers final: 7
  residues processed: 129
  average time/residue: 0.1960
  time to fit residues: 31.8762
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  : 0.490 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 49 optimal weight:    0.0030
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0470
   chunk 13 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.6094

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.163221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.128803 restraints weight = 8085.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.128685 restraints weight = 9584.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.129635 restraints weight = 8076.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3555

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= 0.180
  Angle     :  0.791  20.706   7173  Z= 0.370
  Chirality :  0.053   0.546    834
  Planarity :  0.004   0.026    900
  Dihedral  :  6.021  52.218   1003
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.91 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 19.66 %
    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: -0.15 (0.31), residues: 690
  helix: -1.31 (0.48), residues: 117
  sheet:  1.23 (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 153 
 HIS   0.004   0.001   HIS C 196 
 PHE   0.023   0.002   PHE C 118 
 TYR   0.018   0.002   TYR C  82 
 ARG   0.006   0.001   ARG B 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01257 (   12)
  link_NAG-ASN         : angle       5.68564 (   36)
  hydrogen bonds       : bond        0.04229 (  168)
  hydrogen bonds       : angle       6.72409 (  531)
  SS BOND              : bond        0.00627 (    9)
  SS BOND              : angle       2.44520 (   18)
  covalent geometry    : bond        0.00399 ( 5154)
  covalent geometry    : angle       0.67253 ( 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
  127 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A  229 ARG cc_start: 0.8306 (ttm170) cc_final: 0.7966 (mtm110)
REVERT: A  256 TYR cc_start: 0.8537 (m-80) cc_final: 0.7984 (m-10)
REVERT: B   66 LEU cc_start: 0.9165 (mp) cc_final: 0.8947 (mp)
REVERT: B  191 GLN cc_start: 0.8143 (tp40) cc_final: 0.7374 (tp40)
REVERT: B  229 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7532 (mtm110)
REVERT: B  256 TYR cc_start: 0.8507 (m-80) cc_final: 0.7443 (m-10)
REVERT: C   64 TRP cc_start: 0.8800 (t60) cc_final: 0.8549 (t60)
REVERT: C   80 TRP cc_start: 0.8849 (p90) cc_final: 0.8351 (p90)
REVERT: C  152 LEU cc_start: 0.7933 (mt) cc_final: 0.7640 (mt)
REVERT: C  229 ARG cc_start: 0.8703 (ttm170) cc_final: 0.7693 (mtm110)
REVERT: C  256 TYR cc_start: 0.8273 (m-80) cc_final: 0.7836 (m-10)
  outliers start: 19
  outliers final: 10
  residues processed: 119
  average time/residue: 0.1910
  time to fit residues: 28.1571
Evaluate side-chains
  115 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.162704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.128903 restraints weight = 8235.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.128725 restraints weight = 9109.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.130374 restraints weight = 8099.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5175  Z= 0.137
  Angle     :  0.739  18.754   7173  Z= 0.336
  Chirality :  0.052   0.547    834
  Planarity :  0.004   0.025    900
  Dihedral  :  5.797  47.143   1003
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.93 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 20.80 %
    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: -0.12 (0.31), residues: 690
  helix: -0.89 (0.51), residues: 114
  sheet:  1.04 (0.35), residues: 198
  loop : -0.38 (0.31), residues: 378

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   0.025   0.002   PHE C 118 
 TYR   0.018   0.002   TYR B 168 
 ARG   0.003   0.000   ARG C 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01262 (   12)
  link_NAG-ASN         : angle       5.77598 (   36)
  hydrogen bonds       : bond        0.03647 (  168)
  hydrogen bonds       : angle       6.37877 (  531)
  SS BOND              : bond        0.00321 (    9)
  SS BOND              : angle       2.00130 (   18)
  covalent geometry    : bond        0.00300 ( 5154)
  covalent geometry    : angle       0.61001 ( 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: 21
    poor density    : 110
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ARG cc_start: 0.8338 (ttm170) cc_final: 0.7638 (mtm110)
REVERT: A  256 TYR cc_start: 0.8503 (m-80) cc_final: 0.7952 (m-10)
REVERT: B   66 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8875 (mp)
REVERT: B  191 GLN cc_start: 0.8351 (tp40) cc_final: 0.7550 (tp40)
REVERT: B  229 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.6965 (mtm110)
REVERT: C   80 TRP cc_start: 0.8841 (p90) cc_final: 0.8276 (p90)
REVERT: C  229 ARG cc_start: 0.8598 (ttm170) cc_final: 0.7697 (mtm110)
REVERT: C  256 TYR cc_start: 0.8273 (m-80) cc_final: 0.7844 (m-10)
  outliers start: 21
  outliers final: 12
  residues processed: 124
  average time/residue: 0.1991
  time to fit residues: 30.3619
Evaluate side-chains
  116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
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  164 LEU
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  182 VAL
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0050
   chunk 59 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.8000

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.162837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.129503 restraints weight = 8227.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.129203 restraints weight = 9490.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.130421 restraints weight = 7062.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5175  Z= 0.123
  Angle     :  0.708  18.452   7173  Z= 0.325
  Chirality :  0.051   0.510    834
  Planarity :  0.004   0.025    900
  Dihedral  :  5.778  43.217   1003
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.77 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 22.51 %
    Favored  : 72.08 %
  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: -0.67 (0.53), residues: 114
  sheet:  1.00 (0.35), residues: 198
  loop : -0.35 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  64 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.022   0.002   PHE C 118 
 TYR   0.024   0.002   TYR C 232 
 ARG   0.009   0.001   ARG A 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00983 (   12)
  link_NAG-ASN         : angle       5.33787 (   36)
  hydrogen bonds       : bond        0.03495 (  168)
  hydrogen bonds       : angle       6.19627 (  531)
  SS BOND              : bond        0.00574 (    9)
  SS BOND              : angle       1.81357 (   18)
  covalent geometry    : bond        0.00264 ( 5154)
  covalent geometry    : angle       0.59329 ( 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
  122 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7527 (mtm110)
REVERT: B   66 LEU cc_start: 0.9148 (mp) cc_final: 0.8897 (mp)
REVERT: B  168 TYR cc_start: 0.8192 (t80) cc_final: 0.7803 (t80)
REVERT: B  191 GLN cc_start: 0.8491 (tp40) cc_final: 0.7684 (tp40)
REVERT: B  229 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.6752 (mtm110)
REVERT: C   80 TRP cc_start: 0.8747 (p90) cc_final: 0.8298 (p90)
REVERT: C  191 GLN cc_start: 0.8525 (tp40) cc_final: 0.7659 (tp40)
REVERT: C  229 ARG cc_start: 0.8597 (ttm170) cc_final: 0.7707 (mtm110)
REVERT: C  256 TYR cc_start: 0.8251 (m-80) cc_final: 0.7862 (m-10)
  outliers start: 19
  outliers final: 11
  residues processed: 115
  average time/residue: 0.2018
  time to fit residues: 28.4791
Evaluate side-chains
  114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
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  205 VAL
Chi-restraints excluded: chain B residue   64 TRP
Chi-restraints excluded: chain B residue   95 PHE
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 B residue  282 LEU
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  203 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:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 67 optimal weight:    0.2980
   chunk 15 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.157474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.124275 restraints weight = 8216.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123721 restraints weight = 9691.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.124842 restraints weight = 8095.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5175  Z= 0.234
  Angle     :  0.769  16.586   7173  Z= 0.364
  Chirality :  0.051   0.406    834
  Planarity :  0.004   0.042    900
  Dihedral  :  6.287  44.136   1003
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.35 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 21.37 %
    Favored  : 70.94 %
  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: -0.36 (0.31), residues: 690
  helix: -1.15 (0.49), residues: 114
  sheet:  0.64 (0.35), residues: 195
  loop : -0.34 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 153 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.029   0.002   PHE C 118 
 TYR   0.039   0.002   TYR C 232 
 ARG   0.008   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01492 (   12)
  link_NAG-ASN         : angle       5.19519 (   36)
  hydrogen bonds       : bond        0.04104 (  168)
  hydrogen bonds       : angle       6.38603 (  531)
  SS BOND              : bond        0.00541 (    9)
  SS BOND              : angle       2.24806 (   18)
  covalent geometry    : bond        0.00545 ( 5154)
  covalent geometry    : angle       0.66856 ( 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
  123 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.8513 (t-100)
REVERT: B   66 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8767 (mp)
REVERT: B  168 TYR cc_start: 0.8337 (t80) cc_final: 0.7832 (t80)
REVERT: B  191 GLN cc_start: 0.8672 (tp40) cc_final: 0.7772 (tp40)
REVERT: B  229 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.6670 (mtm110)
REVERT: B  232 TYR cc_start: 0.8739 (m-80) cc_final: 0.8392 (m-10)
REVERT: C   80 TRP cc_start: 0.8901 (p90) cc_final: 0.8321 (p90)
REVERT: C  172 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8648 (mttp)
REVERT: C  229 ARG cc_start: 0.8661 (ttm170) cc_final: 0.7708 (mtm110)
REVERT: C  256 TYR cc_start: 0.8373 (m-80) cc_final: 0.8167 (m-10)
REVERT: C  274 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.8031 (t-90)
  outliers start: 27
  outliers final: 17
  residues processed: 111
  average time/residue: 0.2071
  time to fit residues: 28.4933
Evaluate side-chains
  112 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
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   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   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   54 LEU
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  244 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:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0470
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.6084

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.159108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125808 restraints weight = 8021.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.126095 restraints weight = 8421.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.127030 restraints weight = 6996.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5175  Z= 0.168
  Angle     :  0.756  16.722   7173  Z= 0.354
  Chirality :  0.048   0.274    834
  Planarity :  0.004   0.040    900
  Dihedral  :  6.398  57.817   1003
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.06 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 24.79 %
    Favored  : 69.52 %
  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: -0.36 (0.31), residues: 690
  helix: -0.95 (0.51), residues: 114
  sheet:  0.84 (0.37), residues: 180
  loop : -0.49 (0.30), residues: 396

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   0.020   0.002   PHE C 118 
 TYR   0.032   0.002   TYR C 168 
 ARG   0.008   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00605 (   12)
  link_NAG-ASN         : angle       4.78845 (   36)
  hydrogen bonds       : bond        0.03749 (  168)
  hydrogen bonds       : angle       6.18667 (  531)
  SS BOND              : bond        0.00632 (    9)
  SS BOND              : angle       2.87773 (   18)
  covalent geometry    : bond        0.00383 ( 5154)
  covalent geometry    : angle       0.66225 ( 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
  117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.8528 (t-100)
REVERT: A  224 ARG cc_start: 0.8280 (mtp180) cc_final: 0.8078 (ttm170)
REVERT: B   66 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8946 (mp)
REVERT: B  168 TYR cc_start: 0.8367 (t80) cc_final: 0.7940 (t80)
REVERT: B  191 GLN cc_start: 0.8646 (tp40) cc_final: 0.7677 (tp40)
REVERT: B  229 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6654 (mtm110)
REVERT: C   80 TRP cc_start: 0.8819 (p90) cc_final: 0.8413 (p90)
REVERT: C  172 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8632 (mttp)
REVERT: C  229 ARG cc_start: 0.8621 (ttm170) cc_final: 0.7647 (mtm110)
REVERT: C  256 TYR cc_start: 0.8317 (m-80) cc_final: 0.8108 (m-10)
REVERT: C  274 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.6681 (t70)
  outliers start: 20
  outliers final: 14
  residues processed: 108
  average time/residue: 0.2191
  time to fit residues: 29.1499
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  : 0.539 
-------------------------------------------------------------------------------
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   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  279 ILE
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  274 HIS
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:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.160190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.125214 restraints weight = 8089.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.122728 restraints weight = 8136.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123701 restraints weight = 6671.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.4880

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= 0.113
  Angle     :  0.664  10.334   7173  Z= 0.313
  Chirality :  0.047   0.286    834
  Planarity :  0.004   0.031    900
  Dihedral  :  5.609  41.175   1003
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  4.06 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 26.21 %
    Favored  : 68.38 %
  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: -0.30 (0.31), residues: 690
  helix: -0.81 (0.52), residues: 114
  sheet:  0.88 (0.37), residues: 180
  loop : -0.48 (0.30), residues: 396

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   0.019   0.002   PHE B 118 
 TYR   0.030   0.002   TYR C 168 
 ARG   0.007   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00530 (   12)
  link_NAG-ASN         : angle       3.56489 (   36)
  hydrogen bonds       : bond        0.03471 (  168)
  hydrogen bonds       : angle       6.06551 (  531)
  SS BOND              : bond        0.00293 (    9)
  SS BOND              : angle       2.20515 (   18)
  covalent geometry    : bond        0.00252 ( 5154)
  covalent geometry    : angle       0.60607 ( 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
  115 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8913 (OUTLIER) cc_final: 0.8519 (t-100)
REVERT: A  224 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8133 (ttm170)
REVERT: B  168 TYR cc_start: 0.8404 (t80) cc_final: 0.7883 (t80)
REVERT: B  191 GLN cc_start: 0.8511 (tp40) cc_final: 0.7577 (tp40)
REVERT: B  229 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6524 (mtm110)
REVERT: C   80 TRP cc_start: 0.8822 (p90) cc_final: 0.8440 (p90)
REVERT: C  172 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8633 (mttp)
REVERT: C  191 GLN cc_start: 0.8515 (tp40) cc_final: 0.7528 (tp40)
REVERT: C  229 ARG cc_start: 0.8644 (ttm170) cc_final: 0.7574 (mtm110)
REVERT: C  256 TYR cc_start: 0.8348 (m-80) cc_final: 0.8031 (m-10)
REVERT: C  274 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.6799 (t70)
  outliers start: 19
  outliers final: 13
  residues processed: 108
  average time/residue: 0.2044
  time to fit residues: 27.6300
Evaluate side-chains
  107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
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  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain C residue   54 LEU
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:    0.5980
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 = 0.3822 r_free = 0.3822 target = 0.158479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.124811 restraints weight = 7949.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.124701 restraints weight = 9063.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.125760 restraints weight = 7699.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5175  Z= 0.148
  Angle     :  0.655   9.359   7173  Z= 0.316
  Chirality :  0.046   0.218    834
  Planarity :  0.004   0.037    900
  Dihedral  :  5.681  43.054   1003
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.20 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 27.07 %
    Favored  : 67.81 %
  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: -0.46 (0.31), residues: 690
  helix: -0.83 (0.52), residues: 105
  sheet:  0.78 (0.38), residues: 180
  loop : -0.65 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 127 
 HIS   0.006   0.001   HIS C 196 
 PHE   0.021   0.002   PHE A 118 
 TYR   0.029   0.002   TYR C 168 
 ARG   0.011   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00461 (   12)
  link_NAG-ASN         : angle       3.22229 (   36)
  hydrogen bonds       : bond        0.03676 (  168)
  hydrogen bonds       : angle       6.08518 (  531)
  SS BOND              : bond        0.00314 (    9)
  SS BOND              : angle       2.18781 (   18)
  covalent geometry    : bond        0.00347 ( 5154)
  covalent geometry    : angle       0.60688 ( 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
  108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.8551 (t-100)
REVERT: A  224 ARG cc_start: 0.8348 (mtp180) cc_final: 0.8105 (ttm170)
REVERT: A  229 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7278 (mtm-85)
REVERT: B   66 LEU cc_start: 0.9096 (mp) cc_final: 0.8820 (mp)
REVERT: B  168 TYR cc_start: 0.8462 (t80) cc_final: 0.7764 (t80)
REVERT: B  191 GLN cc_start: 0.8607 (tp40) cc_final: 0.7584 (tp40)
REVERT: B  229 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.6568 (mtm110)
REVERT: B  232 TYR cc_start: 0.8694 (m-80) cc_final: 0.8444 (m-10)
REVERT: C   80 TRP cc_start: 0.8831 (p90) cc_final: 0.8452 (p90)
REVERT: C  172 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8662 (mttp)
REVERT: C  229 ARG cc_start: 0.8610 (ttm170) cc_final: 0.7376 (mtm-85)
REVERT: C  256 TYR cc_start: 0.8264 (m-80) cc_final: 0.8057 (m-10)
REVERT: C  274 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.6873 (t70)
  outliers start: 18
  outliers final: 11
  residues processed: 102
  average time/residue: 0.1847
  time to fit residues: 23.4246
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  : 0.501 
-------------------------------------------------------------------------------
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  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
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:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 17 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.159083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.123554 restraints weight = 8352.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121232 restraints weight = 7430.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123067 restraints weight = 5735.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5175  Z= 0.122
  Angle     :  0.644   9.039   7173  Z= 0.309
  Chirality :  0.045   0.170    834
  Planarity :  0.004   0.047    900
  Dihedral  :  5.354  41.129   1003
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  4.06 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.21 %
    Favored  : 67.24 %
  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: -0.43 (0.31), residues: 690
  helix: -0.80 (0.53), residues: 105
  sheet:  0.83 (0.38), residues: 180
  loop : -0.65 (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   0.020   0.002   PHE A 118 
 TYR   0.029   0.002   TYR C 168 
 ARG   0.012   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (   12)
  link_NAG-ASN         : angle       2.99088 (   36)
  hydrogen bonds       : bond        0.03521 (  168)
  hydrogen bonds       : angle       6.00328 (  531)
  SS BOND              : bond        0.00340 (    9)
  SS BOND              : angle       2.32518 (   18)
  covalent geometry    : bond        0.00283 ( 5154)
  covalent geometry    : angle       0.59896 ( 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: 16
    poor density    : 91
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.8525 (t-100)
REVERT: A  229 ARG cc_start: 0.8445 (ttm170) cc_final: 0.7073 (mtm-85)
REVERT: B   66 LEU cc_start: 0.9115 (mp) cc_final: 0.8831 (mp)
REVERT: B  168 TYR cc_start: 0.8596 (t80) cc_final: 0.7845 (t80)
REVERT: B  191 GLN cc_start: 0.8333 (tp40) cc_final: 0.7529 (tp40)
REVERT: B  229 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.6098 (mtm110)
REVERT: B  232 TYR cc_start: 0.8796 (m-80) cc_final: 0.8540 (m-10)
REVERT: C   80 TRP cc_start: 0.8873 (p90) cc_final: 0.8486 (p90)
REVERT: C  152 LEU cc_start: 0.7762 (mt) cc_final: 0.7337 (mt)
REVERT: C  172 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8738 (mttp)
REVERT: C  229 ARG cc_start: 0.8710 (ttm170) cc_final: 0.7168 (mtm-85)
REVERT: C  274 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.6999 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1876
  time to fit residues: 23.5748
Evaluate side-chains
  104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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  236 LEU
Chi-restraints excluded: chain C residue  274 HIS
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:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:    0.3980
   chunk 43 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.158892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125208 restraints weight = 8410.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.126747 restraints weight = 8216.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.128287 restraints weight = 5913.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.5347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5175  Z= 0.117
  Angle     :  0.631   8.188   7173  Z= 0.305
  Chirality :  0.045   0.152    834
  Planarity :  0.004   0.045    900
  Dihedral  :  5.108  40.209   1003
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  3.91 %
    Favored  : 95.22 %
  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: -0.41 (0.31), residues: 690
  helix: -0.74 (0.53), residues: 105
  sheet:  0.84 (0.38), residues: 180
  loop : -0.64 (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   0.021   0.002   PHE B 118 
 TYR   0.027   0.002   TYR C 168 
 ARG   0.012   0.001   ARG B 224 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00415 (   12)
  link_NAG-ASN         : angle       2.77629 (   36)
  hydrogen bonds       : bond        0.03437 (  168)
  hydrogen bonds       : angle       5.94179 (  531)
  SS BOND              : bond        0.00243 (    9)
  SS BOND              : angle       2.09661 (   18)
  covalent geometry    : bond        0.00272 ( 5154)
  covalent geometry    : angle       0.59283 ( 7119)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1954.24 seconds
wall clock time: 34 minutes 51.25 seconds (2091.25 seconds total)