Starting phenix.real_space_refine
on Tue Mar  3 14:25:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rtu_24689/03_2026/7rtu_24689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rtu_24689/03_2026/7rtu_24689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rtu_24689/03_2026/7rtu_24689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rtu_24689/03_2026/7rtu_24689.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rtu_24689/03_2026/7rtu_24689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rtu_24689/03_2026/7rtu_24689.map"
  }
  resolution = 3.89
  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=   0.000 sd=   1.000
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      48      5.16       5
     C    3829      2.51       5
     N     959      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5962
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3053
          Classifications: {'peptide': 395}
          Link IDs: {'PTRANS': 9, 'TRANS': 385}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2755
          Classifications: {'peptide': 359}
          Link IDs: {'PTRANS': 6, 'TRANS': 352}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "D"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.56, per 1000 atoms: 0.26
  Number of scatterers: 5962
  At special positions: 0
  Unit cell: (74.705, 60.21, 223, 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      48     16.00
     O    1126      8.00
     N     959      7.00
     C    3829      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG C   1 " - " ASN A 129 "
      " NAG D   1 " - " ASN A 352 "
      " NAG E   1 " - " ASN B 129 "
      " NAG F   1 " - " ASN B 352 "
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 220.5 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      89.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 19
    Processing helix  chain 'A' and resid 38 through 73
      removed outlier: 3.727A  pdb=" N   LEU A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 162
      removed outlier: 4.419A  pdb=" N   LEU A 150 " --> pdb=" O   MET A 146 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   GLU A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 187
      removed outlier: 4.423A  pdb=" N   THR A 170 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 236
    Processing helix  chain 'A' and resid 245 through 276
      removed outlier: 3.766A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
      removed outlier: 3.553A  pdb=" N   THR A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 299
      removed outlier: 3.530A  pdb=" N   THR A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 333
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 340 through 365
      removed outlier: 4.179A  pdb=" N   GLY A 346 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.486A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 414
      Proline residue:  A 411  - end of helix
      removed outlier: 3.860A  pdb=" N   TRP A 414 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 71
      removed outlier: 4.519A  pdb=" N   SER B  44 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU B  45 " --> pdb=" O   TYR B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 162
      removed outlier: 3.556A  pdb=" N   ILE B 122 " --> pdb=" O   MET B 118 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   THR B 131 " --> pdb=" O   ASN B 127 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASP B 136 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   LEU B 150 " --> pdb=" O   MET B 146 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLU B 151 " --> pdb=" O   LYS B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 188
      removed outlier: 3.711A  pdb=" N   LEU B 188 " --> pdb=" O   GLN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 236
      removed outlier: 3.658A  pdb=" N   THR B 196 " --> pdb=" O   ARG B 192 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLN B 197 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA B 206 " --> pdb=" O   SER B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 244
    Processing helix  chain 'B' and resid 245 through 276
      removed outlier: 4.081A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
    Processing helix  chain 'B' and resid 290 through 299
      removed outlier: 3.718A  pdb=" N   THR B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 333
    Processing helix  chain 'B' and resid 338 through 365
      removed outlier: 3.849A  pdb=" N   LYS B 342 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ASP B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY B 346 " --> pdb=" O   LYS B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 414
      removed outlier: 4.394A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
      Proline residue:  B 411  - end of helix

    547 hydrogen bonds defined for protein.
    1641 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: 0.92

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1866
        1.34 -     1.46: 1093
        1.46 -     1.58: 3048
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 6073
  Sorted by residual:
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.552 -0.033 2.00e-02 2.50e+03 2.70e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.551 -0.032 2.00e-02 2.50e+03 2.58e+00
  bond pdb=" C1  BMA F   3 "
       pdb=" C2  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.546 -0.027 2.00e-02 2.50e+03 1.87e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.67e+00
  ... (remaining 6068 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 8084
        1.69 -     3.37: 133
        3.37 -     5.06: 38
        5.06 -     6.75: 12
        6.75 -     8.44: 2
  Bond angle restraints: 8269
  Sorted by residual:
  angle pdb=" N   VAL B 194 "
        pdb=" CA  VAL B 194 "
        pdb=" C   VAL B 194 "
      ideal   model   delta    sigma   weight residual
     112.96  109.08    3.88 1.00e+00 1.00e+00 1.51e+01
  angle pdb=" CB  MET A 174 "
        pdb=" CG  MET A 174 "
        pdb=" SD  MET A 174 "
      ideal   model   delta    sigma   weight residual
     112.70  104.26    8.44 3.00e+00 1.11e-01 7.91e+00
  angle pdb=" C   LYS B 147 "
        pdb=" N   VAL B 148 "
        pdb=" CA  VAL B 148 "
      ideal   model   delta    sigma   weight residual
     122.97  120.53    2.44 9.80e-01 1.04e+00 6.20e+00
  angle pdb=" C   MET A 174 "
        pdb=" CA  MET A 174 "
        pdb=" CB  MET A 174 "
      ideal   model   delta    sigma   weight residual
     109.99  114.49   -4.50 2.09e+00 2.29e-01 4.64e+00
  angle pdb=" C3  BMA F   3 "
        pdb=" C2  BMA F   3 "
        pdb=" O2  BMA F   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.56    6.39 3.00e+00 1.11e-01 4.53e+00
  ... (remaining 8264 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.27: 3342
       22.27 -    44.54: 280
       44.54 -    66.82: 36
       66.82 -    89.09: 37
       89.09 -   111.36: 25
  Dihedral angle restraints: 3720
    sinusoidal: 1537
      harmonic: 2183
  Sorted by residual:
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 367 "
           pdb=" CB  CYS B 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.08   46.92     1      1.00e+01 1.00e-02 3.04e+01
  dihedral pdb=" C1  NAG D   2 "
           pdb=" C2  NAG D   2 "
           pdb=" C3  NAG D   2 "
           pdb=" O3  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -63.73 -111.36     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" C1  NAG F   2 "
           pdb=" C2  NAG F   2 "
           pdb=" C3  NAG F   2 "
           pdb=" O3  NAG F   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -64.78 -110.31     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 3717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 913
       0.056 -    0.112: 108
       0.112 -    0.168: 9
       0.168 -    0.224: 0
       0.224 -    0.280: 7
  Chirality restraints: 1037
  Sorted by residual:
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 1034 not shown)

  Planarity restraints: 1009
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 381 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.46e+00
        pdb=" C   ILE B 381 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ILE B 381 "    0.010 2.00e-02 2.50e+03
        pdb=" N   CYS B 382 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 337 "   -0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO A 338 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 338 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 338 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 379 "   -0.007 2.00e-02 2.50e+03   1.37e-02 1.87e+00
        pdb=" C   THR A 379 "    0.024 2.00e-02 2.50e+03
        pdb=" O   THR A 379 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 380 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1006 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 179
        2.72 -     3.26: 6387
        3.26 -     3.81: 10502
        3.81 -     4.35: 10390
        4.35 -     4.90: 18898
  Nonbonded interactions: 46356
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 280 "
            pdb=" ND2 ASN A 284 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" O   ILE A   9 "
            pdb=" OH  TYR A 383 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OD1 ASN A 111 "
            pdb=" NH1 ARG A 212 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OD1 ASN B 111 "
            pdb=" NH1 ARG B 212 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" OD1 ASP A 223 "
            pdb=" OG1 THR A 252 "
     model   vdw
     2.293 3.040
  ... (remaining 46351 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 39 through 71 or resid 89 through 414))
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = chain 'D'
  selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.140
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.460
  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:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6089  Z= 0.165
  Angle     :  0.621   8.436   8313  Z= 0.284
  Chirality :  0.042   0.280   1037
  Planarity :  0.003   0.035   1005
  Dihedral  : 20.840 111.361   2304
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.47 %
    Favored  : 99.37 %
  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 are not related in a simple way.
  whole:  4.32 (0.31), residues: 746
  helix:  3.15 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.02 (0.73), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 295 
 TYR   0.010   0.001   TYR B 216 
 PHE   0.013   0.001   PHE A 395 
 TRP   0.013   0.001   TRP A  12 
 HIS   0.004   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6073)
  covalent geometry    : angle       0.60857 ( 8269)
  SS BOND              : bond        0.00424 (    4)
  SS BOND              : angle       0.64752 (    8)
  hydrogen bonds       : bond        0.07108 (  547)
  hydrogen bonds       : angle       3.84594 ( 1641)
  link_BETA1-4         : bond        0.00400 (    8)
  link_BETA1-4         : angle       1.62394 (   24)
  link_NAG-ASN         : bond        0.00341 (    4)
  link_NAG-ASN         : angle       2.58007 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.164 
Fit side-chains
REVERT: B  135 MET cc_start: 0.7798 (ttm) cc_final: 0.7239 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0771
  time to fit residues: 8.5333
Evaluate side-chains
  70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4492 r_free = 0.4492 target = 0.213066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.198971 restraints weight = 6641.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.197356 restraints weight = 11309.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.191096 restraints weight = 10115.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.189669 restraints weight = 8054.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.190458 restraints weight = 6543.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.0784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6089  Z= 0.159
  Angle     :  0.629   6.763   8313  Z= 0.292
  Chirality :  0.042   0.309   1037
  Planarity :  0.003   0.037   1005
  Dihedral  : 15.605  88.694   1044
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 11.30 %
    Favored  : 87.76 %
  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 are not related in a simple way.
  whole:  4.08 (0.30), residues: 746
  helix:  2.98 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.15 (0.72), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 212 
 TYR   0.010   0.001   TYR B 216 
 PHE   0.011   0.001   PHE A 403 
 TRP   0.011   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6073)
  covalent geometry    : angle       0.59636 ( 8269)
  SS BOND              : bond        0.00491 (    4)
  SS BOND              : angle       0.48676 (    8)
  hydrogen bonds       : bond        0.03444 (  547)
  hydrogen bonds       : angle       3.53397 ( 1641)
  link_BETA1-4         : bond        0.00440 (    8)
  link_BETA1-4         : angle       3.25017 (   24)
  link_NAG-ASN         : bond        0.00160 (    4)
  link_NAG-ASN         : angle       2.70719 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B  147 LYS cc_start: 0.7454 (ttmm) cc_final: 0.6957 (ttmt)
  outliers start: 6
  outliers final: 4
  residues processed: 75
  average time/residue: 0.0695
  time to fit residues: 7.0656
Evaluate side-chains
  74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  343 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.207432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.193649 restraints weight = 6694.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.191976 restraints weight = 11759.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.183720 restraints weight = 11048.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.181620 restraints weight = 9084.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.181885 restraints weight = 8125.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6089  Z= 0.214
  Angle     :  0.673   6.853   8313  Z= 0.322
  Chirality :  0.044   0.326   1037
  Planarity :  0.004   0.045   1005
  Dihedral  : 12.478  77.668   1044
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.95 %
    Favored  : 81.16 %
  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 are not related in a simple way.
  whole:  3.65 (0.30), residues: 746
  helix:  2.72 (0.19), residues: 667
  sheet:  None (None), residues: 0
  loop : -0.49 (0.70), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 212 
 TYR   0.018   0.002   TYR B 216 
 PHE   0.008   0.001   PHE A 395 
 TRP   0.010   0.001   TRP B 213 
 HIS   0.007   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 6073)
  covalent geometry    : angle       0.64547 ( 8269)
  SS BOND              : bond        0.00736 (    4)
  SS BOND              : angle       0.69887 (    8)
  hydrogen bonds       : bond        0.03774 (  547)
  hydrogen bonds       : angle       3.68441 ( 1641)
  link_BETA1-4         : bond        0.00529 (    8)
  link_BETA1-4         : angle       2.90051 (   24)
  link_NAG-ASN         : bond        0.00184 (    4)
  link_NAG-ASN         : angle       3.05266 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  181 VAL cc_start: 0.6928 (t) cc_final: 0.6614 (t)
REVERT: B  138 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7993 (mp)
REVERT: B  211 TYR cc_start: 0.5976 (t80) cc_final: 0.5677 (t80)
  outliers start: 12
  outliers final: 5
  residues processed: 89
  average time/residue: 0.0734
  time to fit residues: 8.8767
Evaluate side-chains
  81 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  215 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 70 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 12 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4476 r_free = 0.4476 target = 0.210978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.196966 restraints weight = 6650.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.194416 restraints weight = 11547.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.193531 restraints weight = 11080.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.191777 restraints weight = 10510.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.192693 restraints weight = 8644.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6089  Z= 0.139
  Angle     :  0.584   7.567   8313  Z= 0.272
  Chirality :  0.040   0.293   1037
  Planarity :  0.003   0.042   1005
  Dihedral  : 11.228  70.854   1044
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.90 %
    Favored  : 78.81 %
  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 are not related in a simple way.
  whole:  3.96 (0.30), residues: 746
  helix:  2.93 (0.19), residues: 667
  sheet:  None (None), residues: 0
  loop : -0.48 (0.70), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 295 
 TYR   0.014   0.001   TYR B  66 
 PHE   0.008   0.001   PHE A 395 
 TRP   0.009   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6073)
  covalent geometry    : angle       0.55559 ( 8269)
  SS BOND              : bond        0.00305 (    4)
  SS BOND              : angle       0.96690 (    8)
  hydrogen bonds       : bond        0.03368 (  547)
  hydrogen bonds       : angle       3.48977 ( 1641)
  link_BETA1-4         : bond        0.00515 (    8)
  link_BETA1-4         : angle       2.68936 (   24)
  link_NAG-ASN         : bond        0.00332 (    4)
  link_NAG-ASN         : angle       2.87011 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  147 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7886 (mtmm)
REVERT: A  322 MET cc_start: 0.7897 (tpp) cc_final: 0.7266 (mtt)
REVERT: A  324 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7941 (tt)
REVERT: B  147 LYS cc_start: 0.7430 (ttmm) cc_final: 0.6828 (ttmt)
REVERT: B  298 LEU cc_start: 0.8108 (mm) cc_final: 0.7776 (mm)
REVERT: B  324 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7136 (tt)
REVERT: B  351 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8513 (mm)
  outliers start: 21
  outliers final: 8
  residues processed: 88
  average time/residue: 0.0713
  time to fit residues: 8.7429
Evaluate side-chains
  82 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4482 r_free = 0.4482 target = 0.211893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.201574 restraints weight = 6715.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.187893 restraints weight = 9358.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.186701 restraints weight = 10991.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.187456 restraints weight = 8236.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.187456 restraints weight = 6581.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6089  Z= 0.132
  Angle     :  0.573   8.160   8313  Z= 0.266
  Chirality :  0.040   0.294   1037
  Planarity :  0.003   0.039   1005
  Dihedral  :  9.894  59.960   1044
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.09 %
    Favored  : 77.39 %
  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 are not related in a simple way.
  whole:  4.12 (0.30), residues: 746
  helix:  3.04 (0.19), residues: 667
  sheet:  None (None), residues: 0
  loop : -0.49 (0.69), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.012   0.001   TYR B  66 
 PHE   0.008   0.001   PHE A 395 
 TRP   0.009   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6073)
  covalent geometry    : angle       0.54746 ( 8269)
  SS BOND              : bond        0.00511 (    4)
  SS BOND              : angle       0.62724 (    8)
  hydrogen bonds       : bond        0.03239 (  547)
  hydrogen bonds       : angle       3.43630 ( 1641)
  link_BETA1-4         : bond        0.00586 (    8)
  link_BETA1-4         : angle       2.52859 (   24)
  link_NAG-ASN         : bond        0.00354 (    4)
  link_NAG-ASN         : angle       2.86711 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  322 MET cc_start: 0.7922 (tpp) cc_final: 0.7467 (mtt)
REVERT: A  324 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7897 (tt)
REVERT: B  147 LYS cc_start: 0.7311 (ttmm) cc_final: 0.6694 (ttmt)
REVERT: B  219 LEU cc_start: 0.6817 (tt) cc_final: 0.6430 (tp)
REVERT: B  298 LEU cc_start: 0.8208 (mm) cc_final: 0.7879 (mm)
REVERT: B  324 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7228 (tt)
  outliers start: 16
  outliers final: 7
  residues processed: 82
  average time/residue: 0.0661
  time to fit residues: 7.4135
Evaluate side-chains
  76 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 40 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.4501 r_free = 0.4501 target = 0.213725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.202558 restraints weight = 6552.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.189522 restraints weight = 12097.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.188415 restraints weight = 9172.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.189058 restraints weight = 7284.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.189329 restraints weight = 6663.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6089  Z= 0.157
  Angle     :  0.604   8.312   8313  Z= 0.281
  Chirality :  0.041   0.307   1037
  Planarity :  0.003   0.040   1005
  Dihedral  :  9.027  56.304   1044
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.94 %
    Favored  : 77.24 %
  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 are not related in a simple way.
  whole:  3.99 (0.30), residues: 746
  helix:  2.95 (0.19), residues: 667
  sheet:  None (None), residues: 0
  loop : -0.51 (0.69), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 212 
 TYR   0.011   0.001   TYR B  66 
 PHE   0.009   0.001   PHE A 315 
 TRP   0.010   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6073)
  covalent geometry    : angle       0.57895 ( 8269)
  SS BOND              : bond        0.00594 (    4)
  SS BOND              : angle       0.62249 (    8)
  hydrogen bonds       : bond        0.03342 (  547)
  hydrogen bonds       : angle       3.48012 ( 1641)
  link_BETA1-4         : bond        0.00569 (    8)
  link_BETA1-4         : angle       2.54883 (   24)
  link_NAG-ASN         : bond        0.00285 (    4)
  link_NAG-ASN         : angle       2.97907 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  322 MET cc_start: 0.7976 (tpp) cc_final: 0.7603 (mtt)
REVERT: A  324 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7889 (tt)
REVERT: B  138 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8142 (mp)
REVERT: B  147 LYS cc_start: 0.7284 (ttmm) cc_final: 0.6679 (ttmt)
REVERT: B  219 LEU cc_start: 0.6670 (tt) cc_final: 0.6373 (tp)
REVERT: B  298 LEU cc_start: 0.8282 (mm) cc_final: 0.7898 (mm)
REVERT: B  324 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7247 (tt)
REVERT: B  351 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8506 (mm)
  outliers start: 18
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0753
  time to fit residues: 8.4209
Evaluate side-chains
  83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 24 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.210703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.197544 restraints weight = 6627.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.195802 restraints weight = 10890.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.195141 restraints weight = 10247.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.193902 restraints weight = 9183.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.191446 restraints weight = 7881.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6089  Z= 0.147
  Angle     :  0.589   8.067   8313  Z= 0.275
  Chirality :  0.040   0.303   1037
  Planarity :  0.003   0.040   1005
  Dihedral  :  8.351  56.632   1044
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.94 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.05 (0.30), residues: 746
  helix:  2.99 (0.19), residues: 667
  sheet:  None (None), residues: 0
  loop : -0.52 (0.70), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.010   0.001   TYR B  66 
 PHE   0.008   0.001   PHE A 395 
 TRP   0.010   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6073)
  covalent geometry    : angle       0.56287 ( 8269)
  SS BOND              : bond        0.00534 (    4)
  SS BOND              : angle       0.56678 (    8)
  hydrogen bonds       : bond        0.03304 (  547)
  hydrogen bonds       : angle       3.46868 ( 1641)
  link_BETA1-4         : bond        0.00606 (    8)
  link_BETA1-4         : angle       2.54202 (   24)
  link_NAG-ASN         : bond        0.00333 (    4)
  link_NAG-ASN         : angle       2.98341 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  322 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7618 (mtt)
REVERT: A  324 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7847 (tt)
REVERT: B  138 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8178 (mp)
REVERT: B  147 LYS cc_start: 0.7272 (ttmm) cc_final: 0.6664 (ttmt)
REVERT: B  219 LEU cc_start: 0.6732 (tt) cc_final: 0.6477 (tp)
REVERT: B  298 LEU cc_start: 0.8258 (mm) cc_final: 0.7879 (mm)
REVERT: B  324 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7241 (tt)
REVERT: B  351 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8500 (mm)
  outliers start: 23
  outliers final: 14
  residues processed: 86
  average time/residue: 0.0716
  time to fit residues: 8.4349
Evaluate side-chains
  86 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 28 optimal weight:    0.1980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.214755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.206248 restraints weight = 6516.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.203375 restraints weight = 10822.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.201266 restraints weight = 11390.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.200422 restraints weight = 9287.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.199826 restraints weight = 8541.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6089  Z= 0.140
  Angle     :  0.598   8.919   8313  Z= 0.276
  Chirality :  0.040   0.303   1037
  Planarity :  0.003   0.040   1005
  Dihedral  :  8.007  57.923   1044
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.94 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.13 (0.30), residues: 746
  helix:  3.05 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.47 (0.69), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 295 
 TYR   0.010   0.001   TYR B  66 
 PHE   0.008   0.001   PHE A 395 
 TRP   0.010   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6073)
  covalent geometry    : angle       0.57314 ( 8269)
  SS BOND              : bond        0.00469 (    4)
  SS BOND              : angle       0.53908 (    8)
  hydrogen bonds       : bond        0.03258 (  547)
  hydrogen bonds       : angle       3.45180 ( 1641)
  link_BETA1-4         : bond        0.00613 (    8)
  link_BETA1-4         : angle       2.51193 (   24)
  link_NAG-ASN         : bond        0.00385 (    4)
  link_NAG-ASN         : angle       2.99363 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  322 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7521 (mtt)
REVERT: A  324 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: B  138 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (mp)
REVERT: B  147 LYS cc_start: 0.7247 (ttmm) cc_final: 0.6638 (ttmt)
REVERT: B  219 LEU cc_start: 0.7067 (tt) cc_final: 0.6819 (tp)
REVERT: B  298 LEU cc_start: 0.8026 (mm) cc_final: 0.7662 (mm)
REVERT: B  324 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7227 (tt)
REVERT: B  351 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8583 (mm)
  outliers start: 20
  outliers final: 13
  residues processed: 82
  average time/residue: 0.0745
  time to fit residues: 8.3002
Evaluate side-chains
  84 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0970
   chunk 56 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.4776

-------------------------------------------------------------------------------
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 = 0.4484 r_free = 0.4484 target = 0.212358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.198951 restraints weight = 6650.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.192517 restraints weight = 10330.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.187549 restraints weight = 6988.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.187555 restraints weight = 8432.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.188493 restraints weight = 6336.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6089  Z= 0.129
  Angle     :  0.582  11.831   8313  Z= 0.268
  Chirality :  0.039   0.301   1037
  Planarity :  0.003   0.039   1005
  Dihedral  :  7.575  58.964   1044
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.09 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.24 (0.30), residues: 746
  helix:  3.15 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.40 (0.66), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 295 
 TYR   0.010   0.001   TYR B  66 
 PHE   0.007   0.001   PHE A 395 
 TRP   0.010   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6073)
  covalent geometry    : angle       0.55734 ( 8269)
  SS BOND              : bond        0.00395 (    4)
  SS BOND              : angle       0.49191 (    8)
  hydrogen bonds       : bond        0.03196 (  547)
  hydrogen bonds       : angle       3.43047 ( 1641)
  link_BETA1-4         : bond        0.00641 (    8)
  link_BETA1-4         : angle       2.41932 (   24)
  link_NAG-ASN         : bond        0.00442 (    4)
  link_NAG-ASN         : angle       2.97430 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  324 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7790 (tt)
REVERT: A  339 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.6839 (t)
REVERT: B  138 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8051 (mp)
REVERT: B  147 LYS cc_start: 0.7199 (ttmm) cc_final: 0.6605 (ttmt)
REVERT: B  219 LEU cc_start: 0.6821 (tt) cc_final: 0.6593 (tp)
REVERT: B  298 LEU cc_start: 0.8256 (mm) cc_final: 0.7866 (mm)
REVERT: B  324 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7201 (tt)
REVERT: B  351 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8566 (mm)
  outliers start: 21
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0706
  time to fit residues: 8.0610
Evaluate side-chains
  83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0980
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4484 r_free = 0.4484 target = 0.212093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.197691 restraints weight = 6719.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.194831 restraints weight = 11343.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.193292 restraints weight = 11736.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.192051 restraints weight = 10466.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.193309 restraints weight = 8096.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6089  Z= 0.133
  Angle     :  0.588  11.523   8313  Z= 0.272
  Chirality :  0.039   0.304   1037
  Planarity :  0.003   0.039   1005
  Dihedral  :  7.327  59.189   1044
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 21.04 %
    Favored  : 76.30 %
  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 are not related in a simple way.
  whole:  4.22 (0.30), residues: 746
  helix:  3.14 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.44 (0.66), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 295 
 TYR   0.010   0.001   TYR B  66 
 PHE   0.007   0.001   PHE A 395 
 TRP   0.010   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6073)
  covalent geometry    : angle       0.56374 ( 8269)
  SS BOND              : bond        0.00409 (    4)
  SS BOND              : angle       0.52731 (    8)
  hydrogen bonds       : bond        0.03211 (  547)
  hydrogen bonds       : angle       3.44448 ( 1641)
  link_BETA1-4         : bond        0.00637 (    8)
  link_BETA1-4         : angle       2.35784 (   24)
  link_NAG-ASN         : bond        0.00442 (    4)
  link_NAG-ASN         : angle       2.98808 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  324 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7798 (tt)
REVERT: A  339 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6848 (t)
REVERT: B  138 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8064 (mp)
REVERT: B  147 LYS cc_start: 0.7227 (ttmm) cc_final: 0.6585 (ttmt)
REVERT: B  219 LEU cc_start: 0.7003 (tt) cc_final: 0.6759 (tp)
REVERT: B  298 LEU cc_start: 0.8081 (mm) cc_final: 0.7710 (mm)
REVERT: B  324 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7239 (tt)
REVERT: B  351 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8571 (mm)
  outliers start: 17
  outliers final: 11
  residues processed: 82
  average time/residue: 0.0701
  time to fit residues: 7.8286
Evaluate side-chains
  83 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  324 ILE
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.210871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.197549 restraints weight = 6660.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.192126 restraints weight = 10585.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.186073 restraints weight = 7140.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.186802 restraints weight = 8039.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.186876 restraints weight = 6181.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6089  Z= 0.145
  Angle     :  0.593  10.721   8313  Z= 0.277
  Chirality :  0.039   0.311   1037
  Planarity :  0.003   0.039   1005
  Dihedral  :  7.034  54.663   1044
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 21.04 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.19 (0.30), residues: 746
  helix:  3.11 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.43 (0.66), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 295 
 TYR   0.009   0.001   TYR B  66 
 PHE   0.007   0.001   PHE A 395 
 TRP   0.010   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6073)
  covalent geometry    : angle       0.56937 ( 8269)
  SS BOND              : bond        0.00485 (    4)
  SS BOND              : angle       0.51879 (    8)
  hydrogen bonds       : bond        0.03255 (  547)
  hydrogen bonds       : angle       3.45925 ( 1641)
  link_BETA1-4         : bond        0.00619 (    8)
  link_BETA1-4         : angle       2.32774 (   24)
  link_NAG-ASN         : bond        0.00408 (    4)
  link_NAG-ASN         : angle       3.04280 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 980.56 seconds
wall clock time: 17 minutes 41.28 seconds (1061.28 seconds total)