Starting phenix.real_space_refine
on Thu Jul  2 14:46:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cvt_45966/07_2026/9cvt_45966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cvt_45966/07_2026/9cvt_45966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cvt_45966/07_2026/9cvt_45966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cvt_45966/07_2026/9cvt_45966.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cvt_45966/07_2026/9cvt_45966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cvt_45966/07_2026/9cvt_45966.cif"
  }
  resolution = 4.41
  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=   0.001 sd=   0.005
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
     P     182      5.49       5
     S      32      5.16       5
     C    5046      2.51       5
     N    1608      2.21       5
     O    2029      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8897
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1213
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 2, 'TRANS': 148}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1308
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 3, 'TRANS': 160}
    Chain: "C"
      Number of atoms: 1337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1337
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1308
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 5, 'TRANS': 162}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1851
          Classifications: {'DNA': 91}
          Link IDs: {'rna3p': 90}
    Chain: "J"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1880
          Classifications: {'DNA': 91}
          Link IDs: {'rna3p': 90}
  Time building chain proxies: 1.67, per 1000 atoms: 0.19
  Number of scatterers: 8897
  At special positions: 0
  Unit cell: (83.905, 114.46, 115.915, 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)
     S      32     16.00
     P     182     15.00
     O    2029      8.00
     N    1608      7.00
     C    5046      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 103 " - pdb=" SG  CYS B 103 " distance=2.04

  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
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 284.6 milliseconds
  

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1254

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      72.7% alpha, 0.3% beta
      89 base pairs and 143 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 15
    Processing helix  chain 'A' and resid 23 through 48
    Processing helix  chain 'A' and resid 54 through 63
      removed outlier: 3.966A  pdb=" N   PHE A  58 " --> pdb=" O   ARG A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 83
      removed outlier: 3.758A  pdb=" N   LYS A  71 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 3.847A  pdb=" N   ASN A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 136
    Processing helix  chain 'A' and resid 142 through 153
    Processing helix  chain 'A' and resid 153 through 161
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 22 through 48
      removed outlier: 3.575A  pdb=" N   LEU B  26 " --> pdb=" O   THR B  22 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU B  27 " --> pdb=" O   LYS B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 64
      removed outlier: 3.546A  pdb=" N   PHE B  58 " --> pdb=" O   ARG B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 82
      removed outlier: 4.329A  pdb=" N   LYS B  71 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 100
      removed outlier: 3.931A  pdb=" N   THR B  94 " --> pdb=" O   PRO B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 136
      removed outlier: 3.694A  pdb=" N   VAL B 111 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 146
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 3.574A  pdb=" N   HIS B 157 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 20
    Processing helix  chain 'C' and resid 28 through 39
    Processing helix  chain 'C' and resid 48 through 74
      removed outlier: 3.667A  pdb=" N   ILE C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 132 through 136
      removed outlier: 4.071A  pdb=" N   MET C 136 " --> pdb=" O   ARG C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 158
    Processing helix  chain 'C' and resid 166 through 195
    Processing helix  chain 'C' and resid 201 through 213
    Processing helix  chain 'D' and resid 28 through 40
      removed outlier: 3.672A  pdb=" N   THR D  32 " --> pdb=" O   PRO D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 75
      removed outlier: 3.541A  pdb=" N   ILE D  52 " --> pdb=" O   THR D  48 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU D  73 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA D  74 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 91
      removed outlier: 3.668A  pdb=" N   MET D  91 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 137
      removed outlier: 4.368A  pdb=" N   LYS D 137 " --> pdb=" O   ARG D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 160
      removed outlier: 4.294A  pdb=" N   PHE D 148 " --> pdb=" O   PRO D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 195
    Processing helix  chain 'D' and resid 201 through 212
      removed outlier: 3.725A  pdb=" N   GLU D 212 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 78 through 79
      removed outlier: 3.639A  pdb=" N   ILE D  79 " --> pdb=" O   HIS D 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1

    335 hydrogen bonds defined for protein.
    990 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      228 hydrogen bonds
      456 hydrogen bond angles
      0 basepair planarities
      89 basepair parallelities
      143 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1617
        1.33 -     1.45: 2952
        1.45 -     1.57: 4430
        1.57 -     1.70: 362
        1.70 -     1.82: 56
  Bond restraints: 9417
  Sorted by residual:
  bond pdb=" C3'  DG J  20 "
       pdb=" C2'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'  DT J -24 "
       pdb=" C2'  DT J -24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'  DA I -22 "
       pdb=" C2'  DA I -22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'  DC J  37 "
       pdb=" C2'  DC J  37 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  bond pdb=" C3'  DA J -15 "
       pdb=" C2'  DA J -15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  ... (remaining 9412 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 12897
        2.04 -     4.09: 521
        4.09 -     6.13: 36
        6.13 -     8.18: 7
        8.18 -    10.22: 3
  Bond angle restraints: 13464
  Sorted by residual:
  angle pdb=" O4'  DG I  28 "
        pdb=" C4'  DG I  28 "
        pdb=" C3'  DG I  28 "
      ideal   model   delta    sigma   weight residual
     106.00  102.82    3.18 6.00e-01 2.78e+00 2.81e+01
  angle pdb=" C   LEU A  97 "
        pdb=" N   MET A  98 "
        pdb=" CA  MET A  98 "
      ideal   model   delta    sigma   weight residual
     120.68  112.41    8.27 1.70e+00 3.46e-01 2.36e+01
  angle pdb=" O4'  DG J -45 "
        pdb=" C1'  DG J -45 "
        pdb=" N9   DG J -45 "
      ideal   model   delta    sigma   weight residual
     108.00  111.31   -3.31 7.00e-01 2.04e+00 2.23e+01
  angle pdb=" O4'  DC I   7 "
        pdb=" C4'  DC I   7 "
        pdb=" C3'  DC I   7 "
      ideal   model   delta    sigma   weight residual
     106.00  103.27    2.73 6.00e-01 2.78e+00 2.06e+01
  angle pdb=" N3   DT J -23 "
        pdb=" C4   DT J -23 "
        pdb=" O4   DT J -23 "
      ideal   model   delta    sigma   weight residual
     119.90  122.56   -2.66 6.00e-01 2.78e+00 1.96e+01
  ... (remaining 13459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.20: 4018
       29.20 -    58.41: 1100
       58.41 -    87.61: 116
       87.61 -   116.81: 7
      116.81 -   146.01: 5
  Dihedral angle restraints: 5246
    sinusoidal: 3337
      harmonic: 1909
  Sorted by residual:
  dihedral pdb=" CB  CYS A 103 "
           pdb=" SG  CYS A 103 "
           pdb=" SG  CYS B 103 "
           pdb=" CB  CYS B 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.15  -83.15     1      1.00e+01 1.00e-02 8.45e+01
  dihedral pdb=" C4'  DC I   4 "
           pdb=" C3'  DC I   4 "
           pdb=" O3'  DC I   4 "
           pdb=" P    DC I   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   73.99  146.01     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" C4'  DC J  37 "
           pdb=" C3'  DC J  37 "
           pdb=" O3'  DC J  37 "
           pdb=" P    DG J  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.06  144.94     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 5243 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1523
       0.112 -    0.224: 37
       0.224 -    0.336: 0
       0.336 -    0.448: 0
       0.448 -    0.560: 1
  Chirality restraints: 1561
  Sorted by residual:
  chirality pdb=" P    DT I -39 "
            pdb=" OP1  DT I -39 "
            pdb=" OP2  DT I -39 "
            pdb=" O5'  DT I -39 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.90   -0.56 2.00e-01 2.50e+01 7.85e+00
  chirality pdb=" CA  CYS B 103 "
            pdb=" N   CYS B 103 "
            pdb=" C   CYS B 103 "
            pdb=" CB  CYS B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.97e-01
  chirality pdb=" CA  GLN C 174 "
            pdb=" N   GLN C 174 "
            pdb=" C   GLN C 174 "
            pdb=" CB  GLN C 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.29e-01
  ... (remaining 1558 not shown)

  Planarity restraints: 1049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 143 "   -0.028 5.00e-02 4.00e+02   4.27e-02 2.91e+00
        pdb=" N   PRO D 144 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D 144 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 144 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  15 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO B  16 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 193 "   -0.012 2.00e-02 2.50e+03   1.05e-02 2.21e+00
        pdb=" CG  TYR D 193 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 193 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 193 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 193 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 193 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 193 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D 193 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1046 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1104
        2.74 -     3.28: 9379
        3.28 -     3.82: 18007
        3.82 -     4.36: 19333
        4.36 -     4.90: 27144
  Nonbonded interactions: 74967
  Sorted by model distance:
  nonbonded pdb=" N   GLN D 135 "
            pdb=" OE1 GLN D 135 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   TYR B 120 "
            pdb=" NE2 GLN B 124 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ILE D 191 "
            pdb=" OG  SER D 194 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OD1 ASP B 153 "
            pdb=" N   LEU B 156 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OE2 GLU B  24 "
            pdb=" OG  SER B  25 "
     model   vdw
     2.242 3.040
  ... (remaining 74962 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'
  selection = (chain 'B' and (resid 9 through 15 or resid 22 through 165))
}
ncs_group {
  reference = (chain 'C' and resid 15 through 212)
  selection = chain 'D'
}

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:             7.340
  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:          0.400
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.060
  Find NCS groups from input model:        0.070
  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:   16.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
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      :  0.006   0.042   9418  Z= 0.502
  Angle     :  0.853  10.222  13466  Z= 0.696
  Chirality :  0.048   0.560   1561
  Planarity :  0.004   0.043   1049
  Dihedral  : 28.597 146.014   3989
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.77 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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:  0.71 (0.33), residues: 641
  helix:  1.41 (0.25), residues: 437
  sheet:  None (None), residues: 0
  loop : -1.63 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 149 
 TYR   0.024   0.002   TYR D 193 
 PHE   0.023   0.002   PHE B 160 
 TRP   0.008   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00581 /  0.50 ( 9417)
  covalent geometry    : angle       0.85333 /  0.70 (13464)
  SS BOND              : bond        0.00586 /  0.31 (    1)
  SS BOND              : angle       0.30687 /  0.18 (    2)
  hydrogen bonds       : bond        0.10808 /  7.31 (  563)
  hydrogen bonds       : angle       4.27635 /  2.98 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9176 (tt) cc_final: 0.8922 (tt)
REVERT: B   31 ASN cc_start: 0.9370 (m110) cc_final: 0.9142 (m110)
REVERT: B  120 TYR cc_start: 0.8981 (t80) cc_final: 0.8750 (t80)
REVERT: B  126 MET cc_start: 0.7816 (ppp) cc_final: 0.7431 (ppp)
REVERT: B  159 MET cc_start: 0.8286 (ptp) cc_final: 0.7896 (ptm)
REVERT: C   79 ILE cc_start: 0.8728 (pt) cc_final: 0.8358 (pt)
REVERT: D   65 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: D   69 LEU cc_start: 0.9100 (mt) cc_final: 0.8793 (mt)
REVERT: D   89 GLU cc_start: 0.9229 (pp20) cc_final: 0.8972 (pp20)
REVERT: D  189 LEU cc_start: 0.9628 (tt) cc_final: 0.8745 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0676
  time to fit residues: 15.7453
Evaluate side-chains
  122 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   30.0000
   overall best weight:    0.8166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
B 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.058334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.042361 restraints weight = 54938.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.043727 restraints weight = 31184.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.044674 restraints weight = 21466.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.045283 restraints weight = 16767.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.045726 restraints weight = 14296.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9418  Z= 0.160
  Angle     :  0.714   7.842  13466  Z= 0.417
  Chirality :  0.048   0.253   1561
  Planarity :  0.005   0.052   1049
  Dihedral  : 32.896 144.841   2656
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.52 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  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:  0.75 (0.33), residues: 641
  helix:  1.39 (0.24), residues: 447
  sheet:  None (None), residues: 0
  loop : -1.65 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  13 
 TYR   0.016   0.002   TYR D 193 
 PHE   0.013   0.001   PHE D 148 
 TRP   0.005   0.001   TRP B  60 
 HIS   0.005   0.001   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.16 ( 9417)
  covalent geometry    : angle       0.71365 /  0.42 (13464)
  SS BOND              : bond        0.00421 /  0.22 (    1)
  SS BOND              : angle       0.83986 /  0.49 (    2)
  hydrogen bonds       : bond        0.04989 /  3.41 (  563)
  hydrogen bonds       : angle       3.58292 /  2.51 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ILE cc_start: 0.7334 (mt) cc_final: 0.7107 (mt)
REVERT: A   46 ILE cc_start: 0.9145 (tt) cc_final: 0.8858 (tt)
REVERT: A   48 ILE cc_start: 0.9324 (tp) cc_final: 0.9116 (tp)
REVERT: A  120 TYR cc_start: 0.9075 (t80) cc_final: 0.8864 (t80)
REVERT: B   31 ASN cc_start: 0.9378 (m110) cc_final: 0.9096 (m-40)
REVERT: B  120 TYR cc_start: 0.8945 (t80) cc_final: 0.8664 (t80)
REVERT: B  126 MET cc_start: 0.7730 (ppp) cc_final: 0.7319 (ppp)
REVERT: C   79 ILE cc_start: 0.8728 (pt) cc_final: 0.8369 (pt)
REVERT: C  174 GLN cc_start: 0.9287 (pm20) cc_final: 0.8968 (pm20)
REVERT: C  178 GLU cc_start: 0.8115 (pp20) cc_final: 0.7734 (pp20)
REVERT: D   65 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8363 (tm-30)
REVERT: D   69 LEU cc_start: 0.9100 (mt) cc_final: 0.8714 (mt)
REVERT: D   96 PHE cc_start: 0.8847 (m-80) cc_final: 0.8632 (m-80)
REVERT: D  210 MET cc_start: 0.8851 (tpt) cc_final: 0.8495 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0607
  time to fit residues: 14.4984
Evaluate side-chains
  119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 80 optimal weight:   30.0000
   chunk 14 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 81 optimal weight:   40.0000
   chunk 7 optimal weight:    9.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A 101 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.057710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.041842 restraints weight = 55363.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.043196 restraints weight = 31793.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.044149 restraints weight = 22074.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.044778 restraints weight = 17260.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.045173 restraints weight = 14687.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9418  Z= 0.161
  Angle     :  0.682   7.497  13466  Z= 0.403
  Chirality :  0.045   0.251   1561
  Planarity :  0.004   0.048   1049
  Dihedral  : 32.922 145.623   2656
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.99 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  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:  0.71 (0.33), residues: 641
  helix:  1.36 (0.24), residues: 447
  sheet:  None (None), residues: 0
  loop : -1.67 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 199 
 TYR   0.015   0.001   TYR D 193 
 PHE   0.014   0.001   PHE D 148 
 TRP   0.005   0.001   TRP B  60 
 HIS   0.006   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.16 ( 9417)
  covalent geometry    : angle       0.68159 /  0.40 (13464)
  SS BOND              : bond        0.00469 /  0.25 (    1)
  SS BOND              : angle       0.44108 /  0.24 (    2)
  hydrogen bonds       : bond        0.04826 /  3.32 (  563)
  hydrogen bonds       : angle       3.45776 /  2.44 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9157 (tt) cc_final: 0.8841 (tt)
REVERT: A   48 ILE cc_start: 0.9337 (tp) cc_final: 0.9118 (tp)
REVERT: A   75 ASP cc_start: 0.9357 (t0) cc_final: 0.9126 (m-30)
REVERT: A  120 TYR cc_start: 0.9085 (t80) cc_final: 0.8695 (t80)
REVERT: B   31 ASN cc_start: 0.9415 (m110) cc_final: 0.9144 (m-40)
REVERT: B  120 TYR cc_start: 0.8958 (t80) cc_final: 0.8654 (t80)
REVERT: B  126 MET cc_start: 0.7737 (ppp) cc_final: 0.7318 (ppp)
REVERT: C   79 ILE cc_start: 0.8728 (pt) cc_final: 0.8414 (pt)
REVERT: C  178 GLU cc_start: 0.8070 (pp20) cc_final: 0.7751 (pp20)
REVERT: D   65 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: D   69 LEU cc_start: 0.9107 (mt) cc_final: 0.8716 (mt)
REVERT: D   89 GLU cc_start: 0.9185 (pp20) cc_final: 0.8973 (pp20)
REVERT: D  189 LEU cc_start: 0.9653 (tt) cc_final: 0.9448 (tt)
REVERT: D  210 MET cc_start: 0.8835 (tpt) cc_final: 0.8464 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0807
  time to fit residues: 18.1661
Evaluate side-chains
  114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:   30.0000
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 70 optimal weight:   30.0000
   chunk 10 optimal weight:    5.9990
   chunk 77 optimal weight:   30.0000
   chunk 54 optimal weight:    6.9990
   chunk 67 optimal weight:   40.0000
   chunk 34 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.057024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.041193 restraints weight = 56280.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.042502 restraints weight = 32036.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.043416 restraints weight = 22234.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.044046 restraints weight = 17460.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.044457 restraints weight = 14856.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9418  Z= 0.176
  Angle     :  0.699   7.508  13466  Z= 0.409
  Chirality :  0.046   0.255   1561
  Planarity :  0.005   0.049   1049
  Dihedral  : 32.943 145.825   2656
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.62 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  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:  0.71 (0.33), residues: 641
  helix:  1.41 (0.24), residues: 447
  sheet:  None (None), residues: 0
  loop : -1.78 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 149 
 TYR   0.014   0.001   TYR D 193 
 PHE   0.022   0.002   PHE A  76 
 TRP   0.005   0.001   TRP A  60 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.18 ( 9417)
  covalent geometry    : angle       0.69926 /  0.41 (13464)
  SS BOND              : bond        0.00263 /  0.14 (    1)
  SS BOND              : angle       0.39316 /  0.22 (    2)
  hydrogen bonds       : bond        0.04853 /  3.33 (  563)
  hydrogen bonds       : angle       3.47867 /  2.44 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.9340 (tp) cc_final: 0.9122 (tp)
REVERT: A   75 ASP cc_start: 0.9419 (t0) cc_final: 0.9169 (m-30)
REVERT: A  120 TYR cc_start: 0.9122 (t80) cc_final: 0.8730 (t80)
REVERT: B   31 ASN cc_start: 0.9429 (m110) cc_final: 0.9141 (m-40)
REVERT: B  120 TYR cc_start: 0.8970 (t80) cc_final: 0.8695 (t80)
REVERT: B  126 MET cc_start: 0.7760 (ppp) cc_final: 0.7331 (ppp)
REVERT: C   79 ILE cc_start: 0.8794 (pt) cc_final: 0.8527 (pt)
REVERT: C  178 GLU cc_start: 0.8084 (pp20) cc_final: 0.7765 (pp20)
REVERT: D   65 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8362 (tm-30)
REVERT: D   69 LEU cc_start: 0.9101 (mt) cc_final: 0.8712 (mt)
REVERT: D  143 ILE cc_start: 0.8843 (tp) cc_final: 0.8574 (tp)
REVERT: D  210 MET cc_start: 0.8880 (tpt) cc_final: 0.8486 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0844
  time to fit residues: 18.9482
Evaluate side-chains
  112 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:   30.0000
   chunk 64 optimal weight:   50.0000
   chunk 42 optimal weight:    3.9990
   chunk 73 optimal weight:   50.0000
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:   30.0000
   chunk 19 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 79 optimal weight:   30.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A  43 GLN
A 101 ASN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.054335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.039356 restraints weight = 55062.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.040636 restraints weight = 31055.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.041529 restraints weight = 21280.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.042130 restraints weight = 16485.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.042546 restraints weight = 13853.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9418  Z= 0.256
  Angle     :  0.780   8.425  13466  Z= 0.448
  Chirality :  0.048   0.241   1561
  Planarity :  0.005   0.057   1049
  Dihedral  : 33.030 148.364   2656
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.24 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  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:  0.30 (0.32), residues: 641
  helix:  1.11 (0.24), residues: 447
  sheet:  None (None), residues: 0
  loop : -1.99 (0.41), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 105 
 TYR   0.018   0.002   TYR D 193 
 PHE   0.036   0.003   PHE B 160 
 TRP   0.006   0.001   TRP A  60 
 HIS   0.006   0.002   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00484 /  0.26 ( 9417)
  covalent geometry    : angle       0.77990 /  0.45 (13464)
  SS BOND              : bond        0.00723 /  0.38 (    1)
  SS BOND              : angle       1.41363 /  0.79 (    2)
  hydrogen bonds       : bond        0.06528 /  4.50 (  563)
  hydrogen bonds       : angle       3.95372 /  2.78 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 TRP cc_start: 0.8868 (m100) cc_final: 0.8619 (m100)
REVERT: A  120 TYR cc_start: 0.9206 (t80) cc_final: 0.8972 (t80)
REVERT: B   31 ASN cc_start: 0.9491 (m110) cc_final: 0.9223 (m110)
REVERT: B  126 MET cc_start: 0.7833 (ppp) cc_final: 0.7420 (ppp)
REVERT: C   79 ILE cc_start: 0.8874 (pt) cc_final: 0.8627 (pt)
REVERT: D   33 GLN cc_start: 0.9116 (mp10) cc_final: 0.8884 (mp10)
REVERT: D   65 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8429 (tm-30)
REVERT: D   69 LEU cc_start: 0.9136 (mt) cc_final: 0.8814 (mt)
REVERT: D  143 ILE cc_start: 0.8950 (tp) cc_final: 0.8698 (tp)
REVERT: D  210 MET cc_start: 0.8942 (tpt) cc_final: 0.8526 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0863
  time to fit residues: 18.4736
Evaluate side-chains
  108 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:   30.0000
   chunk 3 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 71 optimal weight:   30.0000
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 GLN
A 101 ASN
A 124 GLN
B 124 GLN
B 157 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.055266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.040172 restraints weight = 54506.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.041481 restraints weight = 30177.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.042388 restraints weight = 20515.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.042985 restraints weight = 15847.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.043378 restraints weight = 13337.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9418  Z= 0.181
  Angle     :  0.718   8.029  13466  Z= 0.417
  Chirality :  0.047   0.252   1561
  Planarity :  0.005   0.053   1049
  Dihedral  : 33.017 146.364   2656
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.15 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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:  0.50 (0.33), residues: 641
  helix:  1.25 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.89 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  76 
 TYR   0.014   0.002   TYR B 120 
 PHE   0.037   0.002   PHE B 160 
 TRP   0.003   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.18 ( 9417)
  covalent geometry    : angle       0.71806 /  0.42 (13464)
  SS BOND              : bond        0.00564 /  0.30 (    1)
  SS BOND              : angle       1.13957 /  0.66 (    2)
  hydrogen bonds       : bond        0.05211 /  3.60 (  563)
  hydrogen bonds       : angle       3.68585 /  2.61 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ASN cc_start: 0.9457 (m110) cc_final: 0.9191 (m-40)
REVERT: A   60 TRP cc_start: 0.8847 (m100) cc_final: 0.8601 (m100)
REVERT: A   75 ASP cc_start: 0.9420 (t0) cc_final: 0.9188 (m-30)
REVERT: A  120 TYR cc_start: 0.9182 (t80) cc_final: 0.8845 (t80)
REVERT: B   31 ASN cc_start: 0.9470 (m110) cc_final: 0.9195 (m110)
REVERT: B  120 TYR cc_start: 0.9134 (t80) cc_final: 0.8767 (t80)
REVERT: B  126 MET cc_start: 0.7855 (ppp) cc_final: 0.7449 (ppp)
REVERT: C   79 ILE cc_start: 0.8848 (pt) cc_final: 0.8633 (pt)
REVERT: D   65 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8416 (tm-30)
REVERT: D   69 LEU cc_start: 0.9122 (mt) cc_final: 0.8791 (mt)
REVERT: D  143 ILE cc_start: 0.8925 (tp) cc_final: 0.8689 (tp)
REVERT: D  210 MET cc_start: 0.8893 (tpt) cc_final: 0.8459 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0804
  time to fit residues: 17.7695
Evaluate side-chains
  119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 78 optimal weight:   30.0000
   chunk 49 optimal weight:    0.4980
   chunk 6 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 28 optimal weight:    8.9990
   chunk 79 optimal weight:   30.0000
   chunk 53 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    5.0988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.054859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.039227 restraints weight = 57778.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.040502 restraints weight = 33272.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.041376 restraints weight = 23217.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.041977 restraints weight = 18305.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.042334 restraints weight = 15642.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9418  Z= 0.231
  Angle     :  0.759   8.124  13466  Z= 0.439
  Chirality :  0.048   0.246   1561
  Planarity :  0.005   0.055   1049
  Dihedral  : 32.977 146.998   2656
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.40 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  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:  0.22 (0.33), residues: 641
  helix:  1.05 (0.24), residues: 447
  sheet:  None (None), residues: 0
  loop : -2.01 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 149 
 TYR   0.021   0.002   TYR D 193 
 PHE   0.033   0.002   PHE B 160 
 TRP   0.005   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.23 ( 9417)
  covalent geometry    : angle       0.75927 /  0.44 (13464)
  SS BOND              : bond        0.00527 /  0.28 (    1)
  SS BOND              : angle       1.36296 /  0.77 (    2)
  hydrogen bonds       : bond        0.05959 /  4.13 (  563)
  hydrogen bonds       : angle       3.89761 /  2.75 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 TRP cc_start: 0.8920 (m100) cc_final: 0.8666 (m100)
REVERT: A  120 TYR cc_start: 0.9252 (t80) cc_final: 0.8948 (t80)
REVERT: B   28 THR cc_start: 0.9731 (p) cc_final: 0.9529 (p)
REVERT: B   31 ASN cc_start: 0.9494 (m110) cc_final: 0.9203 (m-40)
REVERT: B  120 TYR cc_start: 0.9137 (t80) cc_final: 0.8796 (t80)
REVERT: B  126 MET cc_start: 0.7865 (ppp) cc_final: 0.7459 (ppp)
REVERT: C   79 ILE cc_start: 0.8864 (pt) cc_final: 0.8652 (pt)
REVERT: C  174 GLN cc_start: 0.9227 (pm20) cc_final: 0.8850 (pm20)
REVERT: C  178 GLU cc_start: 0.8169 (pp20) cc_final: 0.7810 (pp20)
REVERT: D   65 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8388 (tm-30)
REVERT: D   69 LEU cc_start: 0.9109 (mt) cc_final: 0.8826 (mt)
REVERT: D  143 ILE cc_start: 0.8986 (tp) cc_final: 0.8748 (tp)
REVERT: D  189 LEU cc_start: 0.9600 (tt) cc_final: 0.9352 (tt)
REVERT: D  210 MET cc_start: 0.8904 (tpt) cc_final: 0.8460 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0866
  time to fit residues: 18.8314
Evaluate side-chains
  112 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 65 optimal weight:   30.0000
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0060
   overall best weight:    2.2002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.055791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.040857 restraints weight = 54146.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.042198 restraints weight = 29889.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.043145 restraints weight = 20199.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.043747 restraints weight = 15417.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.044207 restraints weight = 12913.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9418  Z= 0.158
  Angle     :  0.712   8.230  13466  Z= 0.409
  Chirality :  0.047   0.259   1561
  Planarity :  0.005   0.048   1049
  Dihedral  : 32.941 146.360   2656
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.46 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.92 %
    Favored  : 97.91 %
  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:  0.54 (0.33), residues: 641
  helix:  1.29 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.91 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 149 
 TYR   0.020   0.002   TYR D 193 
 PHE   0.030   0.002   PHE B 160 
 TRP   0.003   0.001   TRP B  60 
 HIS   0.006   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.16 ( 9417)
  covalent geometry    : angle       0.71154 /  0.41 (13464)
  SS BOND              : bond        0.00474 /  0.25 (    1)
  SS BOND              : angle       1.23696 /  0.71 (    2)
  hydrogen bonds       : bond        0.04788 /  3.32 (  563)
  hydrogen bonds       : angle       3.48691 /  2.47 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9339 (tp) cc_final: 0.9059 (tt)
REVERT: A   75 ASP cc_start: 0.9407 (t0) cc_final: 0.9183 (m-30)
REVERT: A   76 PHE cc_start: 0.8811 (m-80) cc_final: 0.8577 (m-10)
REVERT: A  120 TYR cc_start: 0.9217 (t80) cc_final: 0.8907 (t80)
REVERT: B   28 THR cc_start: 0.9712 (p) cc_final: 0.9511 (p)
REVERT: B   31 ASN cc_start: 0.9470 (m110) cc_final: 0.9176 (m-40)
REVERT: B  120 TYR cc_start: 0.9117 (t80) cc_final: 0.8749 (t80)
REVERT: B  126 MET cc_start: 0.7820 (ppp) cc_final: 0.7406 (ppp)
REVERT: C   79 ILE cc_start: 0.8792 (pt) cc_final: 0.8544 (pt)
REVERT: C  178 GLU cc_start: 0.8124 (pp20) cc_final: 0.7763 (pp20)
REVERT: D   65 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8337 (tm-30)
REVERT: D   69 LEU cc_start: 0.9089 (mt) cc_final: 0.8746 (mt)
REVERT: D  210 MET cc_start: 0.8824 (tpt) cc_final: 0.8384 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0896
  time to fit residues: 20.1559
Evaluate side-chains
  116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:   30.0000
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 77 optimal weight:   30.0000
   chunk 40 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 71 optimal weight:   30.0000
   chunk 58 optimal weight:    0.7980
   chunk 76 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9980
   overall best weight:    3.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.055338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.040241 restraints weight = 53878.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.041565 restraints weight = 30111.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.042517 restraints weight = 20525.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.043152 restraints weight = 15732.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.043555 restraints weight = 13148.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9418  Z= 0.175
  Angle     :  0.727   7.713  13466  Z= 0.416
  Chirality :  0.047   0.256   1561
  Planarity :  0.005   0.049   1049
  Dihedral  : 32.917 146.314   2656
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.08 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.35 %
    Favored  : 99.48 %
  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:  0.58 (0.34), residues: 641
  helix:  1.30 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.81 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  13 
 TYR   0.018   0.002   TYR D 193 
 PHE   0.029   0.002   PHE B 160 
 TRP   0.008   0.001   TRP A  60 
 HIS   0.006   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.18 ( 9417)
  covalent geometry    : angle       0.72654 /  0.42 (13464)
  SS BOND              : bond        0.00402 /  0.21 (    1)
  SS BOND              : angle       1.11857 /  0.63 (    2)
  hydrogen bonds       : bond        0.05054 /  3.51 (  563)
  hydrogen bonds       : angle       3.60286 /  2.55 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.8835 (tpt90) cc_final: 0.8493 (mtm-85)
REVERT: A   46 ILE cc_start: 0.9291 (tp) cc_final: 0.9074 (tt)
REVERT: A   76 PHE cc_start: 0.8851 (m-80) cc_final: 0.8538 (m-10)
REVERT: A  120 TYR cc_start: 0.9250 (t80) cc_final: 0.8934 (t80)
REVERT: B   31 ASN cc_start: 0.9482 (m110) cc_final: 0.9196 (m-40)
REVERT: B  120 TYR cc_start: 0.9103 (t80) cc_final: 0.8727 (t80)
REVERT: B  126 MET cc_start: 0.7847 (ppp) cc_final: 0.7440 (ppp)
REVERT: C   79 ILE cc_start: 0.8838 (pt) cc_final: 0.8616 (pt)
REVERT: C   89 GLU cc_start: 0.9179 (tp30) cc_final: 0.8978 (tp30)
REVERT: C  178 GLU cc_start: 0.8155 (pp20) cc_final: 0.7816 (pp20)
REVERT: D   65 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8374 (tm-30)
REVERT: D   69 LEU cc_start: 0.9077 (mt) cc_final: 0.8762 (mt)
REVERT: D  210 MET cc_start: 0.8830 (tpt) cc_final: 0.8412 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0754
  time to fit residues: 16.6337
Evaluate side-chains
  113 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   chunk 40 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 61 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:   30.0000
   chunk 44 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
A 157 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.057585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.041925 restraints weight = 54043.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.043317 restraints weight = 30366.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.044272 restraints weight = 20760.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.044932 restraints weight = 16038.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.045367 restraints weight = 13484.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9418  Z= 0.144
  Angle     :  0.727   9.436  13466  Z= 0.410
  Chirality :  0.047   0.274   1561
  Planarity :  0.004   0.051   1049
  Dihedral  : 32.863 144.017   2656
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.68 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.52 %
    Favored  : 99.30 %
  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:  0.61 (0.33), residues: 641
  helix:  1.30 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.75 (0.44), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  13 
 TYR   0.021   0.002   TYR D 193 
 PHE   0.026   0.002   PHE B 160 
 TRP   0.009   0.001   TRP A  60 
 HIS   0.006   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.14 ( 9417)
  covalent geometry    : angle       0.72681 /  0.41 (13464)
  SS BOND              : bond        0.00433 /  0.23 (    1)
  SS BOND              : angle       1.04136 /  0.60 (    2)
  hydrogen bonds       : bond        0.04376 /  3.03 (  563)
  hydrogen bonds       : angle       3.29280 /  2.34 ( 1446)

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

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

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1282 Ramachandran restraints generated.
    641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ILE cc_start: 0.9307 (tp) cc_final: 0.9004 (tt)
REVERT: A   76 PHE cc_start: 0.8858 (m-80) cc_final: 0.8540 (m-10)
REVERT: A  120 TYR cc_start: 0.9218 (t80) cc_final: 0.8896 (t80)
REVERT: B   31 ASN cc_start: 0.9449 (m110) cc_final: 0.9163 (m-40)
REVERT: B  120 TYR cc_start: 0.9056 (t80) cc_final: 0.8665 (t80)
REVERT: B  126 MET cc_start: 0.7806 (ppp) cc_final: 0.7380 (ppp)
REVERT: C  178 GLU cc_start: 0.8055 (pp20) cc_final: 0.7711 (pp20)
REVERT: D   65 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: D   69 LEU cc_start: 0.9041 (mt) cc_final: 0.8705 (mt)
REVERT: D  149 ARG cc_start: 0.9545 (ttp-110) cc_final: 0.9065 (ttt180)
REVERT: D  189 LEU cc_start: 0.9613 (tt) cc_final: 0.9373 (tt)
REVERT: D  210 MET cc_start: 0.8783 (tpt) cc_final: 0.8429 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0830
  time to fit residues: 19.3837
Evaluate side-chains
  123 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 30 optimal weight:    0.5980
   chunk 1 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 81 optimal weight:   40.0000
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 71 optimal weight:   30.0000
   chunk 47 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 65 optimal weight:   30.0000
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  30 ASN
A 124 GLN
A 157 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.057450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.041869 restraints weight = 54462.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.043272 restraints weight = 30928.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.044231 restraints weight = 21173.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.044897 restraints weight = 16389.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.045324 restraints weight = 13779.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9418  Z= 0.143
  Angle     :  0.716   9.402  13466  Z= 0.404
  Chirality :  0.046   0.271   1561
  Planarity :  0.004   0.048   1049
  Dihedral  : 32.829 144.721   2656
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.84 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.52 %
    Favored  : 99.30 %
  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:  0.65 (0.34), residues: 641
  helix:  1.31 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.69 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 149 
 TYR   0.018   0.002   TYR D 193 
 PHE   0.027   0.002   PHE B 160 
 TRP   0.008   0.001   TRP A  60 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.14 ( 9417)
  covalent geometry    : angle       0.71632 /  0.40 (13464)
  SS BOND              : bond        0.00335 /  0.18 (    1)
  SS BOND              : angle       0.89739 /  0.51 (    2)
  hydrogen bonds       : bond        0.04293 /  2.98 (  563)
  hydrogen bonds       : angle       3.30121 /  2.35 ( 1446)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1915.34 seconds
wall clock time: 33 minutes 43.38 seconds (2023.38 seconds total)