Starting phenix.real_space_refine
on Fri Aug 22 16:58:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxo_36707/08_2025/8jxo_36707_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxo_36707/08_2025/8jxo_36707.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxo_36707/08_2025/8jxo_36707_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxo_36707/08_2025/8jxo_36707_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxo_36707/08_2025/8jxo_36707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxo_36707/08_2025/8jxo_36707.map"
  }
  resolution = 2.7
  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=   0.010
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: 5
    Type Number    sf(0)   Gaussians
     K      18      8.98       5
     S      42      5.16       5
     C    4176      2.51       5
     N     954      2.21       5
     O    1104      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6294
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2069
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 11, 'TRANS': 250}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 26
          Unusual residues: {'  K': 6, 'RET': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    518  SG  CYS A  72      43.541  52.990  56.049  1.00 30.00           S

  Restraints were copied for chains:
    D, E
  Time building chain proxies: 1.47, per 1000 atoms: 0.23
  Number of scatterers: 6294
  At special positions: 0
  Unit cell: (73.85, 73.15, 90.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K      18     19.00
     S      42     16.00
     O    1104      8.00
     N     954      7.00
     C    4176      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 365.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      81.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 12
    Processing helix  chain 'A' and resid 17 through 45
    Processing helix  chain 'A' and resid 59 through 62
    Processing helix  chain 'A' and resid 63 through 89
    Processing helix  chain 'A' and resid 103 through 120
      removed outlier: 4.483A  pdb=" N   ILE A 107 " --> pdb=" O   SER A 103 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 124 through 145
      removed outlier: 3.830A  pdb=" N   VAL A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 174
      removed outlier: 3.626A  pdb=" N   TYR A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR A 152 " --> pdb=" O   PRO A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
      removed outlier: 3.826A  pdb=" N   TRP A 185 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TYR A 186 " --> pdb=" O   SER A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 205
      removed outlier: 3.587A  pdb=" N   PHE A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      Proline residue:  A 202  - end of helix
      removed outlier: 3.533A  pdb=" N   TRP A 205 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 216 through 231
      removed outlier: 3.534A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 263
    Processing helix  chain 'D' and resid 8 through 12
    Processing helix  chain 'D' and resid 17 through 45
    Processing helix  chain 'D' and resid 59 through 62
    Processing helix  chain 'D' and resid 63 through 89
    Processing helix  chain 'D' and resid 103 through 120
      removed outlier: 4.483A  pdb=" N   ILE D 107 " --> pdb=" O   SER D 103 " (cutoff:3.500A)
      Proline residue:  D 110  - end of helix
    Processing helix  chain 'D' and resid 124 through 145
      removed outlier: 3.830A  pdb=" N   VAL D 140 " --> pdb=" O   LEU D 136 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE D 143 " --> pdb=" O   ALA D 139 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 174
      removed outlier: 3.626A  pdb=" N   TYR D 151 " --> pdb=" O   ALA D 147 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR D 152 " --> pdb=" O   PRO D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 196
      removed outlier: 3.826A  pdb=" N   TRP D 185 " --> pdb=" O   ASP D 181 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TYR D 186 " --> pdb=" O   SER D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 205
      removed outlier: 3.587A  pdb=" N   PHE D 201 " --> pdb=" O   GLY D 197 " (cutoff:3.500A)
      Proline residue:  D 202  - end of helix
      removed outlier: 3.532A  pdb=" N   TRP D 205 " --> pdb=" O   PHE D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 216 through 231
      removed outlier: 3.534A  pdb=" N   ILE D 226 " --> pdb=" O   ILE D 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 263
    Processing helix  chain 'E' and resid 8 through 12
    Processing helix  chain 'E' and resid 17 through 45
    Processing helix  chain 'E' and resid 59 through 62
    Processing helix  chain 'E' and resid 63 through 89
    Processing helix  chain 'E' and resid 103 through 120
      removed outlier: 4.483A  pdb=" N   ILE E 107 " --> pdb=" O   SER E 103 " (cutoff:3.500A)
      Proline residue:  E 110  - end of helix
    Processing helix  chain 'E' and resid 124 through 145
      removed outlier: 3.829A  pdb=" N   VAL E 140 " --> pdb=" O   LEU E 136 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE E 143 " --> pdb=" O   ALA E 139 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 146 through 174
      removed outlier: 3.626A  pdb=" N   TYR E 151 " --> pdb=" O   ALA E 147 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR E 152 " --> pdb=" O   PRO E 148 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 196
      removed outlier: 3.826A  pdb=" N   TRP E 185 " --> pdb=" O   ASP E 181 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   TYR E 186 " --> pdb=" O   SER E 182 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 205
      removed outlier: 3.587A  pdb=" N   PHE E 201 " --> pdb=" O   GLY E 197 " (cutoff:3.500A)
      Proline residue:  E 202  - end of helix
      removed outlier: 3.532A  pdb=" N   TRP E 205 " --> pdb=" O   PHE E 201 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 216 through 231
      removed outlier: 3.534A  pdb=" N   ILE E 226 " --> pdb=" O   ILE E 222 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 231 through 263

    456 hydrogen bonds defined for protein.
    1341 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 980
        1.32 -     1.44: 1939
        1.44 -     1.56: 3492
        1.56 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6465
  Sorted by residual:
  bond pdb=" CA  LEU D 192 "
       pdb=" C   LEU D 192 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.053 1.24e-02 6.50e+03 1.80e+01
  bond pdb=" CA  LEU A 192 "
       pdb=" C   LEU A 192 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.053 1.24e-02 6.50e+03 1.80e+01
  bond pdb=" CA  LEU E 192 "
       pdb=" C   LEU E 192 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.052 1.24e-02 6.50e+03 1.79e+01
  bond pdb=" C   ASP A  82 "
       pdb=" O   ASP A  82 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.17e-02 7.31e+03 1.34e+01
  bond pdb=" C   ASP D  82 "
       pdb=" O   ASP D  82 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.17e-02 7.31e+03 1.34e+01
  ... (remaining 6460 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 8322
        2.42 -     4.84: 407
        4.84 -     7.25: 46
        7.25 -     9.67: 39
        9.67 -    12.09: 12
  Bond angle restraints: 8826
  Sorted by residual:
  angle pdb=" N   ALA E 137 "
        pdb=" CA  ALA E 137 "
        pdb=" C   ALA E 137 "
      ideal   model   delta    sigma   weight residual
     113.41  101.85   11.56 1.22e+00 6.72e-01 8.99e+01
  angle pdb=" N   ALA A 137 "
        pdb=" CA  ALA A 137 "
        pdb=" C   ALA A 137 "
      ideal   model   delta    sigma   weight residual
     113.41  101.85   11.56 1.22e+00 6.72e-01 8.98e+01
  angle pdb=" N   ALA D 137 "
        pdb=" CA  ALA D 137 "
        pdb=" C   ALA D 137 "
      ideal   model   delta    sigma   weight residual
     113.41  101.87   11.54 1.22e+00 6.72e-01 8.94e+01
  angle pdb=" N   LEU D 192 "
        pdb=" CA  LEU D 192 "
        pdb=" C   LEU D 192 "
      ideal   model   delta    sigma   weight residual
     110.97  100.70   10.27 1.09e+00 8.42e-01 8.88e+01
  angle pdb=" N   LEU A 192 "
        pdb=" CA  LEU A 192 "
        pdb=" C   LEU A 192 "
      ideal   model   delta    sigma   weight residual
     110.97  100.71   10.26 1.09e+00 8.42e-01 8.87e+01
  ... (remaining 8821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 2925
       17.05 -    34.10: 393
       34.10 -    51.15: 216
       51.15 -    68.19: 96
       68.19 -    85.24: 15
  Dihedral angle restraints: 3645
    sinusoidal: 1371
      harmonic: 2274
  Sorted by residual:
  dihedral pdb=" C   ALA E 147 "
           pdb=" N   ALA E 147 "
           pdb=" CA  ALA E 147 "
           pdb=" CB  ALA E 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.59   11.99     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" C   ALA D 147 "
           pdb=" N   ALA D 147 "
           pdb=" CA  ALA D 147 "
           pdb=" CB  ALA D 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.59   11.99     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" C   ALA A 147 "
           pdb=" N   ALA A 147 "
           pdb=" CA  ALA A 147 "
           pdb=" CB  ALA A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.57   11.97     0      2.50e+00 1.60e-01 2.29e+01
  ... (remaining 3642 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 803
       0.111 -    0.222: 115
       0.222 -    0.332: 24
       0.332 -    0.443: 6
       0.443 -    0.554: 6
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" CA  ALA D 147 "
            pdb=" N   ALA D 147 "
            pdb=" C   ALA D 147 "
            pdb=" CB  ALA D 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.93    0.55 2.00e-01 2.50e+01 7.67e+00
  chirality pdb=" CA  ALA E 147 "
            pdb=" N   ALA E 147 "
            pdb=" C   ALA E 147 "
            pdb=" CB  ALA E 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.93    0.55 2.00e-01 2.50e+01 7.66e+00
  chirality pdb=" CA  ALA A 147 "
            pdb=" N   ALA A 147 "
            pdb=" C   ALA A 147 "
            pdb=" CB  ALA A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.93    0.55 2.00e-01 2.50e+01 7.65e+00
  ... (remaining 951 not shown)

  Planarity restraints: 1095
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS E 109 "   -0.113 5.00e-02 4.00e+02   1.65e-01 4.35e+01
        pdb=" N   PRO E 110 "    0.285 5.00e-02 4.00e+02
        pdb=" CA  PRO E 110 "   -0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO E 110 "   -0.096 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS D 109 "    0.113 5.00e-02 4.00e+02   1.65e-01 4.35e+01
        pdb=" N   PRO D 110 "   -0.285 5.00e-02 4.00e+02
        pdb=" CA  PRO D 110 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO D 110 "    0.096 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 109 "    0.113 5.00e-02 4.00e+02   1.65e-01 4.34e+01
        pdb=" N   PRO A 110 "   -0.284 5.00e-02 4.00e+02
        pdb=" CA  PRO A 110 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A 110 "    0.096 5.00e-02 4.00e+02
  ... (remaining 1092 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.34: 12
        2.34 -     3.04: 4136
        3.04 -     3.74: 12484
        3.74 -     4.44: 20815
        4.44 -     5.14: 31780
  Nonbonded interactions: 69227
  Sorted by model distance:
  nonbonded pdb=" CG  MET A 239 "
            pdb=" K     K A 402 "
     model   vdw
     1.645 3.250
  nonbonded pdb=" CG  MET D 239 "
            pdb=" K     K D 402 "
     model   vdw
     1.645 3.250
  nonbonded pdb=" CG  MET E 239 "
            pdb=" K     K E 402 "
     model   vdw
     1.645 3.250
  nonbonded pdb=" CB  MET E 239 "
            pdb=" K     K E 402 "
     model   vdw
     1.890 3.250
  nonbonded pdb=" CB  MET A 239 "
            pdb=" K     K A 402 "
     model   vdw
     1.890 3.250
  ... (remaining 69222 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'E'
}

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 individual isotropic
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:             24.630
  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:          0.370
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     8.070
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
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      :  0.009   0.053   6468  Z= 0.644
  Angle     :  1.326  12.088   8826  Z= 0.904
  Chirality :  0.095   0.554    954
  Planarity :  0.016   0.165   1095
  Dihedral  : 22.328  85.242   2193
  Min Nonbonded Distance : 1.645

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  1.92 %
    Allowed  :  6.92 %
    Favored  : 91.15 %
  Rotamer:
    Outliers : 24.41 %
    Allowed  : 13.15 %
    Favored  : 62.44 %
  Cbeta Deviations :  0.83 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.26), residues: 780
  helix: -1.58 (0.17), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.35 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 176 
 TYR   0.010   0.002   TYR D 102 
 PHE   0.036   0.003   PHE A 143 
 TRP   0.011   0.002   TRP E 219 
 HIS   0.005   0.002   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00867 ( 6465)
  covalent geometry    : angle       1.32574 ( 8826)
  hydrogen bonds       : bond        0.16354 (  456)
  hydrogen bonds       : angle       6.48797 ( 1341)
  Misc. bond           : bond        0.05191 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 156
    poor density    : 122
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7002 (mp0)
REVERT: D   13 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7039 (mp0)
REVERT: D   86 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7717 (m-80)
REVERT: E   13 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7034 (mp0)
  outliers start: 156
  outliers final: 13
  residues processed: 240
  average time/residue: 0.3980
  time to fit residues: 101.0592
Evaluate side-chains
  103 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain D residue    4 CYS
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   86 TYR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain E residue    4 CYS
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  149 TYR
Chi-restraints excluded: chain E residue  192 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A  87 ASN
A 258 GLN
D  24 ASN
D  87 ASN
D 258 GLN
E  24 ASN
E  87 ASN
E 258 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.141169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.122470 restraints weight = 6423.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.40
r_work: 0.3544 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6468  Z= 0.153
  Angle     :  0.624   8.152   8826  Z= 0.320
  Chirality :  0.040   0.135    954
  Planarity :  0.006   0.075   1095
  Dihedral  :  9.811  69.920    907
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  3.59 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 19.87 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.29), residues: 780
  helix:  1.22 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -0.85 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 150 
 TYR   0.015   0.002   TYR A  86 
 PHE   0.012   0.001   PHE D 195 
 TRP   0.013   0.002   TRP D 184 
 HIS   0.004   0.002   HIS E 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6465)
  covalent geometry    : angle       0.62388 ( 8826)
  hydrogen bonds       : bond        0.04601 (  456)
  hydrogen bonds       : angle       4.16874 ( 1341)
  Misc. bond           : bond        0.00086 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 77
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6934 (mp0)
REVERT: D   13 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6918 (mp0)
REVERT: D  260 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7088 (ttpp)
REVERT: E   13 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6930 (mp0)
REVERT: E   75 MET cc_start: 0.8606 (mtt) cc_final: 0.8345 (mtt)
REVERT: E  260 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7077 (ttpp)
  outliers start: 45
  outliers final: 16
  residues processed: 116
  average time/residue: 0.4239
  time to fit residues: 51.9244
Evaluate side-chains
  99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  124 TYR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain D residue  260 LYS
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  124 TYR
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Chi-restraints excluded: chain E residue  257 GLU
Chi-restraints excluded: chain E residue  260 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  53 HIS
A  98 ASN
D  53 HIS
D  98 ASN
E  53 HIS
E  98 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.135522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.115446 restraints weight = 6325.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.45
r_work: 0.3395 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6468  Z= 0.151
  Angle     :  0.576   8.818   8826  Z= 0.292
  Chirality :  0.039   0.110    954
  Planarity :  0.005   0.059   1095
  Dihedral  :  8.914  75.547    894
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  3.59 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 20.97 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.30), residues: 780
  helix:  2.02 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -0.15 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 243 
 TYR   0.012   0.002   TYR D  86 
 PHE   0.012   0.002   PHE D 195 
 TRP   0.013   0.001   TRP E 219 
 HIS   0.005   0.002   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6465)
  covalent geometry    : angle       0.57596 ( 8826)
  hydrogen bonds       : bond        0.04578 (  456)
  hydrogen bonds       : angle       3.97048 ( 1341)
  Misc. bond           : bond        0.00091 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 76
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6897 (mp0)
REVERT: A   56 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7003 (pm20)
REVERT: A  228 ASP cc_start: 0.8311 (m-30) cc_final: 0.8015 (m-30)
REVERT: D   13 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6868 (mp0)
REVERT: D  228 ASP cc_start: 0.8332 (m-30) cc_final: 0.8063 (m-30)
REVERT: E   13 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6930 (mp0)
REVERT: E   75 MET cc_start: 0.8515 (mtt) cc_final: 0.8225 (mtt)
REVERT: E  228 ASP cc_start: 0.8328 (m-30) cc_final: 0.8016 (m-30)
REVERT: E  260 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7027 (ttpp)
  outliers start: 36
  outliers final: 17
  residues processed: 109
  average time/residue: 0.4481
  time to fit residues: 51.5544
Evaluate side-chains
  92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  124 TYR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  124 TYR
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Chi-restraints excluded: chain E residue  260 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
D  87 ASN
E  87 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.131784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.110737 restraints weight = 6364.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.50
r_work: 0.3332 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6468  Z= 0.190
  Angle     :  0.618  10.851   8826  Z= 0.305
  Chirality :  0.040   0.120    954
  Planarity :  0.005   0.048   1095
  Dihedral  :  9.011  84.390    891
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  2.31 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 20.50 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.30), residues: 780
  helix:  2.05 (0.20), residues: 567
  sheet:  None (None), residues: 0
  loop :  0.30 (0.48), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 176 
 TYR   0.016   0.002   TYR D  86 
 PHE   0.015   0.002   PHE D  78 
 TRP   0.013   0.001   TRP E 184 
 HIS   0.006   0.002   HIS E 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 6465)
  covalent geometry    : angle       0.61814 ( 8826)
  hydrogen bonds       : bond        0.04806 (  456)
  hydrogen bonds       : angle       3.96674 ( 1341)
  Misc. bond           : bond        0.00097 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 71
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7013 (mp0)
REVERT: A   56 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7001 (pm20)
REVERT: A  228 ASP cc_start: 0.8610 (m-30) cc_final: 0.8329 (m-30)
REVERT: D   13 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7010 (mp0)
REVERT: D   56 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7158 (pm20)
REVERT: D  228 ASP cc_start: 0.8644 (m-30) cc_final: 0.8373 (m-30)
REVERT: E   13 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7045 (mp0)
REVERT: E   75 MET cc_start: 0.8693 (mtt) cc_final: 0.8441 (mtt)
REVERT: E  228 ASP cc_start: 0.8682 (m-30) cc_final: 0.8407 (m-30)
REVERT: E  260 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7181 (ttpp)
  outliers start: 36
  outliers final: 18
  residues processed: 102
  average time/residue: 0.5134
  time to fit residues: 54.8959
Evaluate side-chains
  92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  124 TYR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  124 TYR
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Chi-restraints excluded: chain E residue  260 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.134968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.113877 restraints weight = 6408.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.52
r_work: 0.3376 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6468  Z= 0.137
  Angle     :  0.548   9.695   8826  Z= 0.271
  Chirality :  0.038   0.113    954
  Planarity :  0.005   0.045   1095
  Dihedral  :  8.641  83.240    891
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.46 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 21.44 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.29), residues: 780
  helix:  2.30 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop :  0.19 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 243 
 TYR   0.013   0.001   TYR D  86 
 PHE   0.009   0.001   PHE D 195 
 TRP   0.011   0.001   TRP E 184 
 HIS   0.003   0.001   HIS D 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6465)
  covalent geometry    : angle       0.54782 ( 8826)
  hydrogen bonds       : bond        0.04297 (  456)
  hydrogen bonds       : angle       3.86723 ( 1341)
  Misc. bond           : bond        0.00035 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6959 (mp0)
REVERT: A   56 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6926 (pm20)
REVERT: A   61 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8020 (pm20)
REVERT: A  228 ASP cc_start: 0.8329 (m-30) cc_final: 0.8053 (m-30)
REVERT: D   13 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6900 (mp0)
REVERT: D  228 ASP cc_start: 0.8382 (m-30) cc_final: 0.8117 (m-30)
REVERT: E   13 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6910 (mp0)
REVERT: E   61 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8024 (pm20)
REVERT: E  228 ASP cc_start: 0.8407 (m-30) cc_final: 0.8139 (m-30)
REVERT: E  243 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7295 (tmm160)
REVERT: E  260 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7141 (ttpp)
  outliers start: 30
  outliers final: 14
  residues processed: 96
  average time/residue: 0.4897
  time to fit residues: 49.5890
Evaluate side-chains
  90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  124 TYR
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  124 TYR
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Chi-restraints excluded: chain E residue  260 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 73 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
E  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.131447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.110278 restraints weight = 6403.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.51
r_work: 0.3387 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6468  Z= 0.197
  Angle     :  0.609  11.052   8826  Z= 0.298
  Chirality :  0.041   0.120    954
  Planarity :  0.005   0.042   1095
  Dihedral  :  8.716  86.882    887
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  2.69 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 21.91 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.29), residues: 780
  helix:  2.18 (0.20), residues: 567
  sheet:  None (None), residues: 0
  loop :  0.31 (0.46), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 243 
 TYR   0.012   0.002   TYR D  86 
 PHE   0.013   0.002   PHE E  78 
 TRP   0.012   0.001   TRP D 184 
 HIS   0.006   0.002   HIS E 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6465)
  covalent geometry    : angle       0.60867 ( 8826)
  hydrogen bonds       : bond        0.04716 (  456)
  hydrogen bonds       : angle       3.93035 ( 1341)
  Misc. bond           : bond        0.00067 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 67
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7087 (mp0)
REVERT: A   56 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7069 (pm20)
REVERT: A   61 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8195 (pm20)
REVERT: A  228 ASP cc_start: 0.8622 (m-30) cc_final: 0.8369 (m-30)
REVERT: D   13 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7065 (mp0)
REVERT: D   56 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7238 (pm20)
REVERT: D  203 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8154 (tt)
REVERT: D  228 ASP cc_start: 0.8685 (m-30) cc_final: 0.8449 (m-30)
REVERT: E   13 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7097 (mp0)
REVERT: E   61 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (pm20)
REVERT: E  203 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8170 (tt)
REVERT: E  228 ASP cc_start: 0.8708 (m-30) cc_final: 0.8467 (m-30)
REVERT: E  260 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7331 (ttpp)
  outliers start: 31
  outliers final: 16
  residues processed: 95
  average time/residue: 0.5202
  time to fit residues: 52.1815
Evaluate side-chains
  92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  124 TYR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain D residue  203 LEU
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  124 TYR
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Chi-restraints excluded: chain E residue  203 LEU
Chi-restraints excluded: chain E residue  260 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0020
   chunk 61 optimal weight:    5.9990
   chunk 66 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
D  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.136709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.115624 restraints weight = 6274.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.50
r_work: 0.3400 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6468  Z= 0.122
  Angle     :  0.521   9.274   8826  Z= 0.258
  Chirality :  0.037   0.114    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  8.054  82.113    887
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  4.10 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 23.00 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.96 (0.29), residues: 780
  helix:  2.51 (0.20), residues: 570
  sheet:  None (None), residues: 0
  loop :  0.46 (0.46), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 243 
 TYR   0.012   0.001   TYR D  86 
 PHE   0.008   0.001   PHE D  95 
 TRP   0.009   0.001   TRP A 184 
 HIS   0.003   0.001   HIS D 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6465)
  covalent geometry    : angle       0.52137 ( 8826)
  hydrogen bonds       : bond        0.04098 (  456)
  hydrogen bonds       : angle       3.82754 ( 1341)
  Misc. bond           : bond        0.00024 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7923 (pm20)
REVERT: A  136 LEU cc_start: 0.7999 (mt) cc_final: 0.7791 (mm)
REVERT: A  228 ASP cc_start: 0.8239 (m-30) cc_final: 0.7995 (m-30)
REVERT: D   13 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6886 (mp0)
REVERT: D   61 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7890 (pm20)
REVERT: D  228 ASP cc_start: 0.8265 (m-30) cc_final: 0.8028 (m-30)
REVERT: E   61 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7933 (pm20)
REVERT: E  228 ASP cc_start: 0.8298 (m-30) cc_final: 0.8070 (m-30)
REVERT: E  243 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7292 (tmm160)
  outliers start: 23
  outliers final: 11
  residues processed: 88
  average time/residue: 0.5377
  time to fit residues: 50.0581
Evaluate side-chains
  81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.134436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.113132 restraints weight = 6356.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.52
r_work: 0.3369 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6468  Z= 0.144
  Angle     :  0.562  10.666   8826  Z= 0.273
  Chirality :  0.039   0.115    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  7.425  84.797    879
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.21 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.63 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.29), residues: 780
  helix:  2.51 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop :  0.31 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 176 
 TYR   0.012   0.001   TYR D  86 
 PHE   0.009   0.001   PHE D 195 
 TRP   0.011   0.001   TRP E 184 
 HIS   0.004   0.001   HIS D 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6465)
  covalent geometry    : angle       0.56190 ( 8826)
  hydrogen bonds       : bond        0.04280 (  456)
  hydrogen bonds       : angle       3.82507 ( 1341)
  Misc. bond           : bond        0.00030 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6298 (mp0)
REVERT: A  203 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8081 (mm)
REVERT: A  228 ASP cc_start: 0.8368 (m-30) cc_final: 0.8090 (m-30)
REVERT: D   13 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6883 (mp0)
REVERT: D   61 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7925 (pm20)
REVERT: D  228 ASP cc_start: 0.8396 (m-30) cc_final: 0.8144 (m-30)
REVERT: E   13 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6492 (mp0)
REVERT: E  228 ASP cc_start: 0.8414 (m-30) cc_final: 0.8156 (m-30)
  outliers start: 20
  outliers final: 11
  residues processed: 83
  average time/residue: 0.4900
  time to fit residues: 43.2095
Evaluate side-chains
  84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 75 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.134794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.113442 restraints weight = 6349.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.52
r_work: 0.3367 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6468  Z= 0.135
  Angle     :  0.545  10.461   8826  Z= 0.267
  Chirality :  0.038   0.115    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  7.079  85.840    873
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.46 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.16 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.29), residues: 780
  helix:  2.54 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop :  0.36 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 243 
 TYR   0.011   0.001   TYR D  86 
 PHE   0.010   0.001   PHE D  95 
 TRP   0.011   0.001   TRP E 184 
 HIS   0.004   0.001   HIS E 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6465)
  covalent geometry    : angle       0.54454 ( 8826)
  hydrogen bonds       : bond        0.04223 (  456)
  hydrogen bonds       : angle       3.80204 ( 1341)
  Misc. bond           : bond        0.00032 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6429 (mp0)
REVERT: A  203 LEU cc_start: 0.8541 (mp) cc_final: 0.8305 (mm)
REVERT: A  228 ASP cc_start: 0.8403 (m-30) cc_final: 0.8141 (m-30)
REVERT: D   61 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8002 (pm20)
REVERT: D  136 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7883 (mm)
REVERT: D  203 LEU cc_start: 0.8557 (mp) cc_final: 0.8313 (mm)
REVERT: D  228 ASP cc_start: 0.8426 (m-30) cc_final: 0.8187 (m-30)
REVERT: E   13 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6671 (mp0)
REVERT: E   61 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7986 (pm20)
REVERT: E  136 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7848 (mm)
REVERT: E  203 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8335 (mm)
REVERT: E  228 ASP cc_start: 0.8464 (m-30) cc_final: 0.8233 (m-30)
REVERT: E  243 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7648 (tmm160)
  outliers start: 20
  outliers final: 9
  residues processed: 83
  average time/residue: 0.4983
  time to fit residues: 44.0638
Evaluate side-chains
  84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Chi-restraints excluded: chain E residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 77 optimal weight:    9.9990
   chunk 68 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
E  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.134050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.112744 restraints weight = 6237.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.50
r_work: 0.3250 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6468  Z= 0.144
  Angle     :  0.556  10.752   8826  Z= 0.273
  Chirality :  0.039   0.114    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  6.785  86.547    870
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.33 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 23.00 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.91 (0.29), residues: 780
  helix:  2.47 (0.20), residues: 567
  sheet:  None (None), residues: 0
  loop :  0.50 (0.45), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 243 
 TYR   0.011   0.001   TYR D  86 
 PHE   0.010   0.001   PHE A  95 
 TRP   0.011   0.001   TRP A 184 
 HIS   0.004   0.001   HIS E 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6465)
  covalent geometry    : angle       0.55592 ( 8826)
  hydrogen bonds       : bond        0.04311 (  456)
  hydrogen bonds       : angle       3.80893 ( 1341)
  Misc. bond           : bond        0.00037 (    3)

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

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6393 (mp0)
REVERT: A  203 LEU cc_start: 0.8364 (mp) cc_final: 0.8118 (mm)
REVERT: A  228 ASP cc_start: 0.8380 (m-30) cc_final: 0.8117 (m-30)
REVERT: D   13 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6420 (mp0)
REVERT: D   61 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (pm20)
REVERT: D  136 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7709 (mm)
REVERT: D  203 LEU cc_start: 0.8393 (mp) cc_final: 0.8137 (mm)
REVERT: D  228 ASP cc_start: 0.8403 (m-30) cc_final: 0.8154 (m-30)
REVERT: E   13 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6578 (mp0)
REVERT: E   61 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7954 (pm20)
REVERT: E  136 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7689 (mm)
REVERT: E  203 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8164 (mm)
REVERT: E  228 ASP cc_start: 0.8438 (m-30) cc_final: 0.8189 (m-30)
  outliers start: 22
  outliers final: 9
  residues processed: 83
  average time/residue: 0.4694
  time to fit residues: 41.4551
Evaluate side-chains
  81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain D residue   13 GLU
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain D residue  194 PHE
Chi-restraints excluded: chain E residue   13 GLU
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  182 SER
Chi-restraints excluded: chain E residue  194 PHE
Chi-restraints excluded: chain E residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.134761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.113440 restraints weight = 6354.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.51
r_work: 0.3292 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6468  Z= 0.134
  Angle     :  0.546  10.277   8826  Z= 0.269
  Chirality :  0.038   0.115    954
  Planarity :  0.005   0.043   1095
  Dihedral  :  6.724  86.311    870
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  3.33 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 23.94 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.96 (0.29), residues: 780
  helix:  2.54 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop :  0.43 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 243 
 TYR   0.011   0.001   TYR D  86 
 PHE   0.010   0.001   PHE D  95 
 TRP   0.011   0.001   TRP A 184 
 HIS   0.003   0.001   HIS E 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6465)
  covalent geometry    : angle       0.54645 ( 8826)
  hydrogen bonds       : bond        0.04219 (  456)
  hydrogen bonds       : angle       3.78877 ( 1341)
  Misc. bond           : bond        0.00032 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2871.66 seconds
wall clock time: 49 minutes 55.71 seconds (2995.71 seconds total)