Starting phenix.real_space_refine
on Fri Oct 10 13:16:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur7_42486/10_2025/8ur7_42486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur7_42486/10_2025/8ur7_42486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ur7_42486/10_2025/8ur7_42486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur7_42486/10_2025/8ur7_42486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur7_42486/10_2025/8ur7_42486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur7_42486/10_2025/8ur7_42486.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.115
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    3795      2.51       5
     N     999      2.21       5
     O     960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5772
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1882
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 83}
          Link IDs: {'PTRANS': 14, 'TRANS': 248}
          Unresolved non-hydrogen bonds: 240
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 9, 'GLU:plan': 21, 'ASP:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 154
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.40, per 1000 atoms: 0.24
  Number of scatterers: 5772
  At special positions: 0
  Unit cell: (82.8298, 85.686, 119.96, 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     960      8.00
     N     999      7.00
     C    3795      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=2.10
    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=2.18
    Simple disulfide: pdb=" SG  CYS B  59 " - pdb=" SG  CYS B  71 " distance=2.10
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C  71 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 139 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 271 " distance=2.18
    Simple disulfide: pdb=" SG  CYS C 107 " - pdb=" SG  CYS C 271 " distance=2.18

  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  58 "
      " NAG A 502 " - " ASN A 163 "
      " NAG A 503 " - " ASN A 129 "
      " NAG B 501 " - " ASN B  58 "
      " NAG B 502 " - " ASN B 163 "
      " NAG B 503 " - " ASN B 129 "
      " NAG C 501 " - " ASN C  58 "
      " NAG C 502 " - " ASN C 163 "
      " NAG C 503 " - " ASN C 129 "
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 244.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1470

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      27.0% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 101 through 109
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 270 through 313
    Processing helix  chain 'B' and resid 60 through 67
    Processing helix  chain 'B' and resid 101 through 109
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 270 through 313
    Processing helix  chain 'C' and resid 60 through 67
    Processing helix  chain 'C' and resid 101 through 109
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 270 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141
      removed outlier: 4.469A  pdb=" N   CYS A 139 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER A 146 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.478A  pdb=" N   TYR B 256 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   LEU B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141
      removed outlier: 4.470A  pdb=" N   CYS B 139 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER B 146 " --> pdb=" O   CYS B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 169
    Processing sheet with id=AA9, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.479A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   LEU C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 119
      removed outlier: 6.479A  pdb=" N   TYR C 256 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141
      removed outlier: 4.470A  pdb=" N   CYS C 139 " --> pdb=" O   SER C 146 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   SER C 146 " --> pdb=" O   CYS C 139 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 169

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

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1182
        1.33 -     1.45: 1482
        1.45 -     1.57: 3267
        1.57 -     1.69: 3
        1.69 -     1.81: 18
  Bond restraints: 5952
  Sorted by residual:
  bond pdb=" C   ALA C  52 "
       pdb=" N   PRO C  53 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 9.40e-03 1.13e+04 7.48e+00
  bond pdb=" C5  NAG A 501 "
       pdb=" O5  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.33e+00
  bond pdb=" C5  NAG C 501 "
       pdb=" O5  NAG C 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.29e+00
  bond pdb=" C   ALA A  52 "
       pdb=" N   PRO A  53 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 9.40e-03 1.13e+04 7.28e+00
  bond pdb=" C5  NAG B 501 "
       pdb=" O5  NAG B 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.28e+00
  ... (remaining 5947 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 6974
        1.63 -     3.25: 1014
        3.25 -     4.88: 106
        4.88 -     6.50: 66
        6.50 -     8.13: 27
  Bond angle restraints: 8187
  Sorted by residual:
  angle pdb=" C   HIS A 184 "
        pdb=" N   PRO A 185 "
        pdb=" CA  PRO A 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.50   -6.84 7.30e-01 1.88e+00 8.79e+01
  angle pdb=" C   HIS B 184 "
        pdb=" N   PRO B 185 "
        pdb=" CA  PRO B 185 "
      ideal   model   delta    sigma   weight residual
     119.66  126.48   -6.82 7.30e-01 1.88e+00 8.73e+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  126.44   -6.78 7.30e-01 1.88e+00 8.63e+01
  angle pdb=" C   ASN B  88 "
        pdb=" N   PRO B  89 "
        pdb=" CA  PRO B  89 "
      ideal   model   delta    sigma   weight residual
     120.31  127.70   -7.39 9.80e-01 1.04e+00 5.69e+01
  angle pdb=" C   ASN A  88 "
        pdb=" N   PRO A  89 "
        pdb=" CA  PRO A  89 "
      ideal   model   delta    sigma   weight residual
     120.31  127.67   -7.36 9.80e-01 1.04e+00 5.63e+01
  ... (remaining 8182 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 3396
       17.27 -    34.53: 87
       34.53 -    51.80: 18
       51.80 -    69.07: 0
       69.07 -    86.33: 9
  Dihedral angle restraints: 3510
    sinusoidal: 1212
      harmonic: 2298
  Sorted by residual:
  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  173.12  -80.12     1      1.00e+01 1.00e-02 7.95e+01
  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  173.11  -80.11     1      1.00e+01 1.00e-02 7.95e+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  173.10  -80.10     1      1.00e+01 1.00e-02 7.95e+01
  ... (remaining 3507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 659
       0.065 -    0.130: 210
       0.130 -    0.194: 52
       0.194 -    0.259: 18
       0.259 -    0.324: 9
  Chirality restraints: 948
  Sorted by residual:
  chirality pdb=" C2  NAG C 502 "
            pdb=" C1  NAG C 502 "
            pdb=" C3  NAG C 502 "
            pdb=" N2  NAG C 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" C2  NAG B 502 "
            pdb=" C1  NAG B 502 "
            pdb=" C3  NAG B 502 "
            pdb=" N2  NAG B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.81    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C2  NAG A 502 "
            pdb=" C1  NAG A 502 "
            pdb=" C3  NAG A 502 "
            pdb=" N2  NAG A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.81    0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 945 not shown)

  Planarity restraints: 1041
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 232 "    0.025 2.00e-02 2.50e+03   1.36e-02 3.72e+00
        pdb=" CG  TYR C 232 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 232 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 232 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 232 "    0.025 2.00e-02 2.50e+03   1.36e-02 3.71e+00
        pdb=" CG  TYR B 232 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 232 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 232 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 232 "    0.025 2.00e-02 2.50e+03   1.36e-02 3.68e+00
        pdb=" CG  TYR A 232 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 232 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 232 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 232 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 232 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1038 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 529
        2.75 -     3.28: 5585
        3.28 -     3.82: 9305
        3.82 -     4.36: 10789
        4.36 -     4.90: 17958
  Nonbonded interactions: 44166
  Sorted by model distance:
  nonbonded pdb=" CB  PRO A  53 "
            pdb=" CE1 TYR A  82 "
     model   vdw
     2.207 3.740
  nonbonded pdb=" CB  PRO B  53 "
            pdb=" CE1 TYR B  82 "
     model   vdw
     2.207 3.740
  nonbonded pdb=" CB  PRO C  53 "
            pdb=" CE1 TYR C  82 "
     model   vdw
     2.207 3.740
  nonbonded pdb=" O   GLU A 309 "
            pdb=" N   ASN A 312 "
     model   vdw
     2.399 3.120
  nonbonded pdb=" O   GLU C 309 "
            pdb=" N   ASN C 312 "
     model   vdw
     2.399 3.120
  ... (remaining 44161 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.130
  Find NCS groups from input model:        0.050
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
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      :  0.010   0.151   5970  Z= 0.577
  Angle     :  1.291   8.129   8232  Z= 0.894
  Chirality :  0.075   0.324    948
  Planarity :  0.005   0.018   1032
  Dihedral  :  9.351  86.333   2013
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  3.31 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.27), residues: 783
  helix:  0.32 (0.34), residues: 201
  sheet:  1.20 (0.31), residues: 198
  loop : -1.30 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 117 
 TYR   0.025   0.005   TYR B 232 
 PHE   0.013   0.003   PHE B 115 
 TRP   0.016   0.003   TRP C  80 
 HIS   0.003   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00917 ( 5952)
  covalent geometry    : angle       1.27745 ( 8187)
  SS BOND              : bond        0.09473 (    9)
  SS BOND              : angle       3.80456 (   18)
  hydrogen bonds       : bond        0.18673 (  285)
  hydrogen bonds       : angle       8.48611 (  864)
  link_NAG-ASN         : bond        0.05673 (    9)
  link_NAG-ASN         : angle       1.97272 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 TYR cc_start: 0.9012 (t80) cc_final: 0.8386 (t80)
REVERT: B  172 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8595 (mmtt)
REVERT: B  223 VAL cc_start: 0.9057 (t) cc_final: 0.8570 (p)
REVERT: B  229 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8225 (mmt90)
REVERT: B  295 HIS cc_start: 0.8473 (t70) cc_final: 0.7975 (t-170)
REVERT: C  102 TYR cc_start: 0.9060 (t80) cc_final: 0.8738 (t80)
REVERT: C  147 PHE cc_start: 0.6582 (t80) cc_final: 0.6143 (t80)
REVERT: C  172 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8519 (mmmt)
  outliers start: 3
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1005
  time to fit residues: 19.8324
Evaluate side-chains
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
B 108 GLN
C 130 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.184856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.152800 restraints weight = 8174.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.151126 restraints weight = 11069.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.153151 restraints weight = 8649.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.153575 restraints weight = 6221.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153848 restraints weight = 6075.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5970  Z= 0.168
  Angle     :  0.637   7.018   8232  Z= 0.339
  Chirality :  0.046   0.190    948
  Planarity :  0.004   0.032   1032
  Dihedral  :  7.318  98.800   1038
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.47 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.29), residues: 783
  helix:  1.63 (0.37), residues: 210
  sheet:  1.21 (0.32), residues: 204
  loop : -1.17 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 305 
 TYR   0.013   0.001   TYR C 195 
 PHE   0.026   0.002   PHE A 115 
 TRP   0.006   0.001   TRP C 153 
 HIS   0.002   0.001   HIS C 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 5952)
  covalent geometry    : angle       0.61729 ( 8187)
  SS BOND              : bond        0.00344 (    9)
  SS BOND              : angle       1.24404 (   18)
  hydrogen bonds       : bond        0.07111 (  285)
  hydrogen bonds       : angle       6.21345 (  864)
  link_NAG-ASN         : bond        0.00544 (    9)
  link_NAG-ASN         : angle       2.63923 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LEU cc_start: 0.8148 (mp) cc_final: 0.7633 (tp)
REVERT: C  168 TYR cc_start: 0.7910 (t80) cc_final: 0.7380 (t80)
REVERT: C  172 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8562 (mmtt)
  outliers start: 11
  outliers final: 10
  residues processed: 115
  average time/residue: 0.0879
  time to fit residues: 12.7867
Evaluate side-chains
  98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  302 HIS
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0470
   chunk 33 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 6 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
A 170 ASN
A 191 GLN
A 250 ASN
B 191 GLN
B 250 ASN
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 191 GLN
C 250 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.185465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.154617 restraints weight = 8210.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.153084 restraints weight = 11153.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.154289 restraints weight = 9192.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.154260 restraints weight = 8542.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.155125 restraints weight = 7199.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5970  Z= 0.126
  Angle     :  0.559   8.217   8232  Z= 0.297
  Chirality :  0.044   0.221    948
  Planarity :  0.004   0.026   1032
  Dihedral  :  6.940  98.477   1038
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 13.25 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.29), residues: 783
  helix:  2.07 (0.36), residues: 210
  sheet:  1.14 (0.34), residues: 195
  loop : -1.16 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 117 
 TYR   0.015   0.001   TYR A 195 
 PHE   0.027   0.002   PHE A 115 
 TRP   0.006   0.001   TRP B 153 
 HIS   0.008   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5952)
  covalent geometry    : angle       0.54515 ( 8187)
  SS BOND              : bond        0.00409 (    9)
  SS BOND              : angle       1.31520 (   18)
  hydrogen bonds       : bond        0.05770 (  285)
  hydrogen bonds       : angle       5.60647 (  864)
  link_NAG-ASN         : bond        0.00311 (    9)
  link_NAG-ASN         : angle       1.99797 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8640 (mp) cc_final: 0.8371 (mp)
REVERT: A  106 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8181 (tmm-80)
REVERT: B  300 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9085 (tt)
REVERT: C  168 TYR cc_start: 0.7947 (t80) cc_final: 0.7534 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0781
  time to fit residues: 10.9032
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0050
   chunk 52 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.1198

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

Flipped N/Q/H residues before XYZ refinement:
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 130 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.180420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.149228 restraints weight = 8249.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147553 restraints weight = 10181.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.148024 restraints weight = 8753.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.148179 restraints weight = 7443.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150656 restraints weight = 6669.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111   5970  Z= 0.170
  Angle     :  0.577   8.447   8232  Z= 0.307
  Chirality :  0.045   0.255    948
  Planarity :  0.004   0.025   1032
  Dihedral  :  6.800  95.255   1038
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 14.79 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.29), residues: 783
  helix:  1.80 (0.37), residues: 210
  sheet:  0.96 (0.36), residues: 189
  loop : -1.13 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 305 
 TYR   0.018   0.001   TYR A 195 
 PHE   0.026   0.002   PHE A 115 
 TRP   0.008   0.001   TRP B 127 
 HIS   0.007   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 5952)
  covalent geometry    : angle       0.56215 ( 8187)
  SS BOND              : bond        0.00711 (    9)
  SS BOND              : angle       1.86638 (   18)
  hydrogen bonds       : bond        0.05628 (  285)
  hydrogen bonds       : angle       5.62717 (  864)
  link_NAG-ASN         : bond        0.00226 (    9)
  link_NAG-ASN         : angle       1.85755 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8678 (mp) cc_final: 0.8472 (mp)
REVERT: B   82 TYR cc_start: 0.7091 (p90) cc_final: 0.6667 (p90)
REVERT: C  106 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.7954 (ttp-170)
  outliers start: 20
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0820
  time to fit residues: 9.7837
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  302 HIS
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0870
   chunk 69 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
A 108 GLN
C 130 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.181123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.149049 restraints weight = 8326.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.146770 restraints weight = 13271.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.148518 restraints weight = 9929.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.149248 restraints weight = 7000.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.149364 restraints weight = 7386.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   5970  Z= 0.152
  Angle     :  0.608   9.336   8232  Z= 0.320
  Chirality :  0.046   0.283    948
  Planarity :  0.004   0.024   1032
  Dihedral  :  6.811  93.264   1038
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.11 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.30), residues: 783
  helix:  1.95 (0.38), residues: 204
  sheet:  0.88 (0.37), residues: 189
  loop : -1.07 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 305 
 TYR   0.021   0.001   TYR A 195 
 PHE   0.026   0.002   PHE A 115 
 TRP   0.007   0.001   TRP B 127 
 HIS   0.007   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5952)
  covalent geometry    : angle       0.58371 ( 8187)
  SS BOND              : bond        0.00516 (    9)
  SS BOND              : angle       3.14351 (   18)
  hydrogen bonds       : bond        0.05385 (  285)
  hydrogen bonds       : angle       5.68606 (  864)
  link_NAG-ASN         : bond        0.00243 (    9)
  link_NAG-ASN         : angle       1.72637 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8729 (mp) cc_final: 0.8426 (mp)
REVERT: A  106 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8077 (tmm-80)
REVERT: B   82 TYR cc_start: 0.7305 (p90) cc_final: 0.6943 (p90)
REVERT: C  106 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8103 (ttp-170)
REVERT: C  305 ARG cc_start: 0.7682 (mmt90) cc_final: 0.7358 (tpp-160)
  outliers start: 12
  outliers final: 10
  residues processed: 89
  average time/residue: 0.0895
  time to fit residues: 10.1693
Evaluate side-chains
  82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0970
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
C 130 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.181506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.151927 restraints weight = 8334.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.149776 restraints weight = 11983.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.150621 restraints weight = 10103.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.151076 restraints weight = 8145.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.151461 restraints weight = 7140.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5970  Z= 0.125
  Angle     :  0.574   8.552   8232  Z= 0.298
  Chirality :  0.044   0.195    948
  Planarity :  0.003   0.023   1032
  Dihedral  :  6.538  89.187   1038
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.01 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.30), residues: 783
  helix:  2.08 (0.39), residues: 207
  sheet:  0.90 (0.38), residues: 189
  loop : -1.03 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 305 
 TYR   0.021   0.001   TYR C 195 
 PHE   0.025   0.002   PHE A 115 
 TRP   0.007   0.001   TRP B 180 
 HIS   0.006   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5952)
  covalent geometry    : angle       0.55669 ( 8187)
  SS BOND              : bond        0.00364 (    9)
  SS BOND              : angle       2.39925 (   18)
  hydrogen bonds       : bond        0.04758 (  285)
  hydrogen bonds       : angle       5.50076 (  864)
  link_NAG-ASN         : bond        0.00223 (    9)
  link_NAG-ASN         : angle       1.67238 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8710 (mp) cc_final: 0.8408 (mp)
REVERT: A  106 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8054 (tmm-80)
REVERT: A  208 HIS cc_start: 0.7130 (m90) cc_final: 0.6835 (m90)
REVERT: B   82 TYR cc_start: 0.7256 (p90) cc_final: 0.6905 (p90)
REVERT: B  102 TYR cc_start: 0.9286 (t80) cc_final: 0.8833 (t80)
REVERT: C  305 ARG cc_start: 0.7530 (mmt90) cc_final: 0.7309 (tpp-160)
  outliers start: 12
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0853
  time to fit residues: 9.6730
Evaluate side-chains
  79 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0030
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0770
   overall best weight:    0.4948

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

Flipped N/Q/H residues before XYZ refinement:
C 130 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.182112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.151874 restraints weight = 8386.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.149899 restraints weight = 14792.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.150649 restraints weight = 11718.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150889 restraints weight = 8754.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153437 restraints weight = 7797.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5970  Z= 0.117
  Angle     :  0.566   8.548   8232  Z= 0.291
  Chirality :  0.044   0.199    948
  Planarity :  0.003   0.024   1032
  Dihedral  :  6.399  85.907   1038
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.34 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.30), residues: 783
  helix:  2.12 (0.39), residues: 207
  sheet:  1.00 (0.44), residues: 147
  loop : -1.02 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 106 
 TYR   0.023   0.001   TYR A 195 
 PHE   0.027   0.002   PHE A 115 
 TRP   0.007   0.001   TRP B 180 
 HIS   0.005   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5952)
  covalent geometry    : angle       0.55122 ( 8187)
  SS BOND              : bond        0.00333 (    9)
  SS BOND              : angle       2.07328 (   18)
  hydrogen bonds       : bond        0.04453 (  285)
  hydrogen bonds       : angle       5.42275 (  864)
  link_NAG-ASN         : bond        0.00273 (    9)
  link_NAG-ASN         : angle       1.65586 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8714 (mp) cc_final: 0.8429 (mp)
REVERT: A  106 ARG cc_start: 0.8782 (ttp-110) cc_final: 0.7982 (tmm-80)
REVERT: A  208 HIS cc_start: 0.6802 (m90) cc_final: 0.6498 (m90)
REVERT: B   66 LEU cc_start: 0.8671 (mp) cc_final: 0.8457 (mt)
REVERT: B   82 TYR cc_start: 0.7208 (p90) cc_final: 0.6907 (p90)
REVERT: B  102 TYR cc_start: 0.9276 (t80) cc_final: 0.8806 (t80)
REVERT: C  106 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.8066 (ttp-170)
REVERT: C  305 ARG cc_start: 0.7485 (mmt90) cc_final: 0.7281 (tpp-160)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0915
  time to fit residues: 9.7604
Evaluate side-chains
  81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 57 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0060
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.180985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.150603 restraints weight = 8278.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.148971 restraints weight = 11338.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.149355 restraints weight = 9873.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.149498 restraints weight = 7865.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.150780 restraints weight = 7049.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5970  Z= 0.123
  Angle     :  0.570   8.556   8232  Z= 0.295
  Chirality :  0.044   0.179    948
  Planarity :  0.003   0.025   1032
  Dihedral  :  6.244  81.244   1038
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.56 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.30), residues: 783
  helix:  2.10 (0.39), residues: 207
  sheet:  0.96 (0.44), residues: 147
  loop : -1.06 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 106 
 TYR   0.025   0.001   TYR A 195 
 PHE   0.028   0.002   PHE A 115 
 TRP   0.007   0.001   TRP B 180 
 HIS   0.005   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5952)
  covalent geometry    : angle       0.55404 ( 8187)
  SS BOND              : bond        0.00351 (    9)
  SS BOND              : angle       2.16866 (   18)
  hydrogen bonds       : bond        0.04405 (  285)
  hydrogen bonds       : angle       5.38769 (  864)
  link_NAG-ASN         : bond        0.00207 (    9)
  link_NAG-ASN         : angle       1.66305 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8632 (mp) cc_final: 0.8399 (mp)
REVERT: A  102 TYR cc_start: 0.9371 (t80) cc_final: 0.8868 (t80)
REVERT: A  106 ARG cc_start: 0.8803 (ttp-110) cc_final: 0.7879 (tmm-80)
REVERT: B   66 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8522 (mt)
REVERT: B   82 TYR cc_start: 0.7216 (p90) cc_final: 0.6922 (p90)
REVERT: B  102 TYR cc_start: 0.9297 (t80) cc_final: 0.8871 (t80)
REVERT: B  106 ARG cc_start: 0.8627 (tmm-80) cc_final: 0.8359 (ttp-110)
REVERT: B  255 TRP cc_start: 0.8348 (t60) cc_final: 0.8079 (t60)
REVERT: C  106 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8126 (ttp-170)
REVERT: C  304 GLU cc_start: 0.8105 (tp30) cc_final: 0.7295 (tp30)
REVERT: C  305 ARG cc_start: 0.7494 (mmt90) cc_final: 0.7277 (tpp-160)
  outliers start: 10
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0804
  time to fit residues: 9.0512
Evaluate side-chains
  86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 70 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.178793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.148344 restraints weight = 8469.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.146701 restraints weight = 12127.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147363 restraints weight = 9984.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147430 restraints weight = 8126.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.148110 restraints weight = 7859.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5970  Z= 0.134
  Angle     :  0.575   8.889   8232  Z= 0.297
  Chirality :  0.044   0.200    948
  Planarity :  0.003   0.025   1032
  Dihedral  :  6.104  77.356   1038
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.30 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.56 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.30), residues: 783
  helix:  1.92 (0.39), residues: 207
  sheet:  0.94 (0.44), residues: 147
  loop : -1.07 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 305 
 TYR   0.024   0.001   TYR C 195 
 PHE   0.028   0.002   PHE A 115 
 TRP   0.008   0.001   TRP B 180 
 HIS   0.004   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5952)
  covalent geometry    : angle       0.55773 ( 8187)
  SS BOND              : bond        0.00371 (    9)
  SS BOND              : angle       2.23484 (   18)
  hydrogen bonds       : bond        0.04527 (  285)
  hydrogen bonds       : angle       5.40443 (  864)
  link_NAG-ASN         : bond        0.00256 (    9)
  link_NAG-ASN         : angle       1.74919 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8615 (mp) cc_final: 0.8337 (mp)
REVERT: A  102 TYR cc_start: 0.9379 (t80) cc_final: 0.8870 (t80)
REVERT: A  106 ARG cc_start: 0.8742 (ttp-110) cc_final: 0.7925 (tmm-80)
REVERT: B   82 TYR cc_start: 0.7096 (p90) cc_final: 0.6782 (p90)
REVERT: B  102 TYR cc_start: 0.9331 (t80) cc_final: 0.8899 (t80)
REVERT: B  106 ARG cc_start: 0.8686 (tmm-80) cc_final: 0.8413 (ttp-110)
REVERT: B  255 TRP cc_start: 0.8387 (t60) cc_final: 0.8070 (t60)
REVERT: C  304 GLU cc_start: 0.8156 (tp30) cc_final: 0.7790 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0839
  time to fit residues: 9.2706
Evaluate side-chains
  82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0270
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.178665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.148614 restraints weight = 8485.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.146776 restraints weight = 11233.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.147600 restraints weight = 10060.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.148356 restraints weight = 7693.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.148590 restraints weight = 7074.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5970  Z= 0.120
  Angle     :  0.567   9.251   8232  Z= 0.292
  Chirality :  0.044   0.177    948
  Planarity :  0.003   0.027   1032
  Dihedral  :  5.990  74.063   1038
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.30 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.78 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.30), residues: 783
  helix:  1.88 (0.38), residues: 207
  sheet:  0.96 (0.44), residues: 147
  loop : -1.10 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 305 
 TYR   0.023   0.001   TYR C 195 
 PHE   0.029   0.002   PHE A 115 
 TRP   0.009   0.001   TRP B  80 
 HIS   0.005   0.001   HIS B 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5952)
  covalent geometry    : angle       0.55178 ( 8187)
  SS BOND              : bond        0.00300 (    9)
  SS BOND              : angle       2.07956 (   18)
  hydrogen bonds       : bond        0.04395 (  285)
  hydrogen bonds       : angle       5.37385 (  864)
  link_NAG-ASN         : bond        0.00208 (    9)
  link_NAG-ASN         : angle       1.72578 (   27)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8661 (mp) cc_final: 0.8353 (mp)
REVERT: A  102 TYR cc_start: 0.9362 (t80) cc_final: 0.8863 (t80)
REVERT: A  106 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.7904 (tmm-80)
REVERT: B   82 TYR cc_start: 0.7084 (p90) cc_final: 0.6753 (p90)
REVERT: B  102 TYR cc_start: 0.9316 (t80) cc_final: 0.8868 (t80)
REVERT: B  106 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8403 (ttp-110)
REVERT: B  255 TRP cc_start: 0.8345 (t60) cc_final: 0.8041 (t60)
  outliers start: 8
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0825
  time to fit residues: 9.4924
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue  170 ASN
Chi-restraints excluded: chain C residue  307 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4012 r_free = 0.4012 target = 0.177053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.147814 restraints weight = 8361.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146452 restraints weight = 13956.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.146520 restraints weight = 11965.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.146690 restraints weight = 10399.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.148305 restraints weight = 8698.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.4951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5970  Z= 0.175
  Angle     :  0.616   9.159   8232  Z= 0.324
  Chirality :  0.045   0.209    948
  Planarity :  0.004   0.028   1032
  Dihedral  :  6.002  69.998   1038
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  2.30 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 17.44 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.30), residues: 783
  helix:  1.64 (0.39), residues: 207
  sheet:  0.79 (0.45), residues: 147
  loop : -1.19 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 106 
 TYR   0.024   0.002   TYR C 195 
 PHE   0.029   0.002   PHE A 115 
 TRP   0.009   0.001   TRP C  80 
 HIS   0.005   0.001   HIS A 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 5952)
  covalent geometry    : angle       0.59587 ( 8187)
  SS BOND              : bond        0.00428 (    9)
  SS BOND              : angle       2.74642 (   18)
  hydrogen bonds       : bond        0.04924 (  285)
  hydrogen bonds       : angle       5.53974 (  864)
  link_NAG-ASN         : bond        0.00250 (    9)
  link_NAG-ASN         : angle       1.78443 (   27)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 981.10 seconds
wall clock time: 17 minutes 33.72 seconds (1053.72 seconds total)