Starting phenix.real_space_refine
on Thu Jul  2 03:14:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sks_40566/07_2026/8sks_40566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sks_40566/07_2026/8sks_40566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sks_40566/07_2026/8sks_40566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sks_40566/07_2026/8sks_40566.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sks_40566/07_2026/8sks_40566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sks_40566/07_2026/8sks_40566.map"
  }
  resolution = 2.91
  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=   0.019
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
     Mn      4      7.51       5
     S      16      5.16       5
     C    3992      2.51       5
     N    1092      2.21       5
     O    1128      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  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: 6232
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1557
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 0
          Ad-hoc single atom residues: {' MN': 1}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.32, per 1000 atoms: 0.21
  Number of scatterers: 6232
  At special positions: 0
  Unit cell: (71.69, 86.67, 86.67, 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)
     Mn      4     24.99
     S      16     16.00
     O    1128      8.00
     N    1092      7.00
     C    3992      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=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 363.5 milliseconds
  

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      69.2% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 39
      removed outlier: 4.275A  pdb=" N   LEU A  38 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A  39 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 76
      removed outlier: 3.915A  pdb=" N   HIS A  55 " --> pdb=" O   HIS A  51 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ALA A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 105
      Proline residue:  A  86  - end of helix
      removed outlier: 3.627A  pdb=" N   THR A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 127 through 142
    Processing helix  chain 'A' and resid 169 through 174
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 196 through 205
      removed outlier: 3.517A  pdb=" N   TYR A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 222
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 4.276A  pdb=" N   LEU B  38 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU B  39 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 76
      removed outlier: 3.914A  pdb=" N   HIS B  55 " --> pdb=" O   HIS B  51 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ALA B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 105
      Proline residue:  B  86  - end of helix
      removed outlier: 3.628A  pdb=" N   THR B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 126
    Processing helix  chain 'B' and resid 127 through 142
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 189 through 194
    Processing helix  chain 'B' and resid 196 through 205
      removed outlier: 3.516A  pdb=" N   TYR B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 222
    Processing helix  chain 'C' and resid 34 through 39
      removed outlier: 4.276A  pdb=" N   LEU C  38 " --> pdb=" O   TYR C  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU C  39 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 76
      removed outlier: 3.915A  pdb=" N   HIS C  55 " --> pdb=" O   HIS C  51 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ALA C  56 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 105
      Proline residue:  C  86  - end of helix
      removed outlier: 3.627A  pdb=" N   THR C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 126
    Processing helix  chain 'C' and resid 127 through 142
    Processing helix  chain 'C' and resid 169 through 174
    Processing helix  chain 'C' and resid 185 through 188
    Processing helix  chain 'C' and resid 189 through 194
    Processing helix  chain 'C' and resid 196 through 205
      removed outlier: 3.517A  pdb=" N   TYR C 200 " --> pdb=" O   VAL C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 222
    Processing helix  chain 'D' and resid 34 through 39
      removed outlier: 4.275A  pdb=" N   LEU D  38 " --> pdb=" O   TYR D  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU D  39 " --> pdb=" O   GLY D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 76
      removed outlier: 3.915A  pdb=" N   HIS D  55 " --> pdb=" O   HIS D  51 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ALA D  56 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 105
      Proline residue:  D  86  - end of helix
      removed outlier: 3.628A  pdb=" N   THR D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 126
    Processing helix  chain 'D' and resid 127 through 142
    Processing helix  chain 'D' and resid 169 through 174
    Processing helix  chain 'D' and resid 185 through 188
    Processing helix  chain 'D' and resid 189 through 194
    Processing helix  chain 'D' and resid 196 through 205
      removed outlier: 3.517A  pdb=" N   TYR D 200 " --> pdb=" O   VAL D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 222
    Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 165
      removed outlier: 7.322A  pdb=" N   GLY A 146 " --> pdb=" O   ASP A 183 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ASP A 183 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLY A 148 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY A 181 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A 150 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 165
      removed outlier: 7.323A  pdb=" N   GLY B 146 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASP B 183 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLY B 148 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY B 181 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU B 150 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 165
      removed outlier: 7.323A  pdb=" N   GLY C 146 " --> pdb=" O   ASP C 183 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ASP C 183 " --> pdb=" O   GLY C 146 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLY C 148 " --> pdb=" O   GLY C 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY C 181 " --> pdb=" O   GLY C 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU C 150 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 165
      removed outlier: 7.322A  pdb=" N   GLY D 146 " --> pdb=" O   ASP D 183 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ASP D 183 " --> pdb=" O   GLY D 146 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLY D 148 " --> pdb=" O   GLY D 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY D 181 " --> pdb=" O   GLY D 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU D 150 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2041
        1.34 -     1.46: 1253
        1.46 -     1.57: 3094
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 6412
  Sorted by residual:
  bond pdb=" CA  LYS D 221 "
       pdb=" C   LYS D 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.508  0.016 1.28e-02 6.10e+03 1.61e+00
  bond pdb=" CA  VAL A 196 "
       pdb=" CB  VAL A 196 "
    ideal  model  delta    sigma   weight residual
    1.527  1.543 -0.016 1.31e-02 5.83e+03 1.45e+00
  bond pdb=" CA  LYS C 221 "
       pdb=" C   LYS C 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.015 1.28e-02 6.10e+03 1.45e+00
  bond pdb=" CA  LYS B 221 "
       pdb=" C   LYS B 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.015 1.28e-02 6.10e+03 1.45e+00
  bond pdb=" CA  VAL B 196 "
       pdb=" CB  VAL B 196 "
    ideal  model  delta    sigma   weight residual
    1.527  1.542 -0.016 1.31e-02 5.83e+03 1.41e+00
  ... (remaining 6407 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 8176
        0.98 -     1.97: 419
        1.97 -     2.95: 89
        2.95 -     3.93: 28
        3.93 -     4.92: 12
  Bond angle restraints: 8724
  Sorted by residual:
  angle pdb=" C   VAL A 196 "
        pdb=" N   ARG A 197 "
        pdb=" CA  ARG A 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.62   -4.53 1.25e+00 6.40e-01 1.31e+01
  angle pdb=" C   VAL B 196 "
        pdb=" N   ARG B 197 "
        pdb=" CA  ARG B 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.61   -4.52 1.25e+00 6.40e-01 1.31e+01
  angle pdb=" C   VAL D 196 "
        pdb=" N   ARG D 197 "
        pdb=" CA  ARG D 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.61   -4.52 1.25e+00 6.40e-01 1.31e+01
  angle pdb=" C   VAL C 196 "
        pdb=" N   ARG C 197 "
        pdb=" CA  ARG C 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.58   -4.49 1.25e+00 6.40e-01 1.29e+01
  angle pdb=" N   VAL C 184 "
        pdb=" CA  VAL C 184 "
        pdb=" C   VAL C 184 "
      ideal   model   delta    sigma   weight residual
     112.29  109.52    2.77 9.40e-01 1.13e+00 8.66e+00
  ... (remaining 8719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 3408
       16.49 -    32.99: 256
       32.99 -    49.48: 28
       49.48 -    65.98: 8
       65.98 -    82.47: 4
  Dihedral angle restraints: 3704
    sinusoidal: 1448
      harmonic: 2256
  Sorted by residual:
  dihedral pdb=" CA  TRP B 149 "
           pdb=" C   TRP B 149 "
           pdb=" N   LEU B 150 "
           pdb=" CA  LEU B 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.65   18.35     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  TRP C 149 "
           pdb=" C   TRP C 149 "
           pdb=" N   LEU C 150 "
           pdb=" CA  LEU C 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.70   18.30     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  TRP D 149 "
           pdb=" C   TRP D 149 "
           pdb=" N   LEU D 150 "
           pdb=" CA  LEU D 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.71   18.29     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 467
       0.026 -    0.052: 286
       0.052 -    0.078: 111
       0.078 -    0.104: 24
       0.104 -    0.131: 16
  Chirality restraints: 904
  Sorted by residual:
  chirality pdb=" CA  ILE A 182 "
            pdb=" N   ILE A 182 "
            pdb=" C   ILE A 182 "
            pdb=" CB  ILE A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE C 182 "
            pdb=" N   ILE C 182 "
            pdb=" C   ILE C 182 "
            pdb=" CB  ILE C 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE D 182 "
            pdb=" N   ILE D 182 "
            pdb=" C   ILE D 182 "
            pdb=" CB  ILE D 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 901 not shown)

  Planarity restraints: 1140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 197 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO D 198 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 198 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 198 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 197 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO B 198 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 198 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 198 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 197 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO C 198 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 198 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 198 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1137 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 36
        2.48 -     3.09: 4537
        3.09 -     3.69: 9955
        3.69 -     4.30: 15215
        4.30 -     4.90: 25365
  Nonbonded interactions: 55108
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 183 "
            pdb="MN    MN C 301 "
     model   vdw
     1.880 3.060
  nonbonded pdb=" OD2 ASP B 183 "
            pdb="MN    MN B 301 "
     model   vdw
     1.881 3.060
  nonbonded pdb=" OD2 ASP D 183 "
            pdb="MN    MN D 301 "
     model   vdw
     1.881 3.060
  nonbonded pdb=" OD2 ASP A 183 "
            pdb="MN    MN A 301 "
     model   vdw
     1.881 3.060
  nonbonded pdb=" NE2 HIS D  50 "
            pdb="MN    MN D 301 "
     model   vdw
     2.017 3.140
  ... (remaining 55103 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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 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:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.310
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:6.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
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      :  0.004   0.028   6412  Z= 0.183
  Angle     :  0.551   4.917   8724  Z= 0.324
  Chirality :  0.039   0.131    904
  Planarity :  0.004   0.039   1140
  Dihedral  : 11.977  82.471   2272
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.81 (0.29), residues: 784
  helix:  0.78 (0.23), residues: 504
  sheet:  1.20 (0.52), residues: 72
  loop : -0.02 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 197 
 TYR   0.023   0.002   TYR C  69 
 PHE   0.005   0.001   PHE B  90 
 TRP   0.009   0.001   TRP A 147 
 HIS   0.004   0.001   HIS D 187 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.18 ( 6412)
  covalent geometry    : angle       0.55137 /  0.32 ( 8724)
  hydrogen bonds       : bond        0.14553 /  9.68 (  404)
  hydrogen bonds       : angle       7.48488 /  5.34 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: A  124 ASP cc_start: 0.8531 (m-30) cc_final: 0.8160 (m-30)
REVERT: A  200 TYR cc_start: 0.9364 (t80) cc_final: 0.9120 (t80)
REVERT: B   70 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: B  124 ASP cc_start: 0.8508 (m-30) cc_final: 0.8105 (m-30)
REVERT: B  200 TYR cc_start: 0.9356 (t80) cc_final: 0.9143 (t80)
REVERT: C   70 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7924 (tm-30)
REVERT: C  124 ASP cc_start: 0.8491 (m-30) cc_final: 0.8071 (m-30)
REVERT: C  200 TYR cc_start: 0.9358 (t80) cc_final: 0.9097 (t80)
REVERT: D   70 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: D  124 ASP cc_start: 0.8481 (m-30) cc_final: 0.8072 (m-30)
REVERT: D  200 TYR cc_start: 0.9355 (t80) cc_final: 0.9142 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.6092
  time to fit residues: 82.9894
Evaluate side-chains
  105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0020
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.089276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.080397 restraints weight = 11827.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.01
r_work: 0.2972 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6412  Z= 0.140
  Angle     :  0.527   4.925   8724  Z= 0.284
  Chirality :  0.039   0.125    904
  Planarity :  0.004   0.039   1140
  Dihedral  :  7.343  87.128    844
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.54 %
    Favored  : 90.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.13 (0.30), residues: 784
  helix:  0.88 (0.23), residues: 508
  sheet:  1.35 (0.56), residues: 80
  loop :  0.46 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 156 
 TYR   0.009   0.001   TYR B  69 
 PHE   0.005   0.001   PHE C  90 
 TRP   0.009   0.001   TRP D 147 
 HIS   0.002   0.001   HIS D 187 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 6412)
  covalent geometry    : angle       0.52661 /  0.28 ( 8724)
  hydrogen bonds       : bond        0.04247 /  2.86 (  404)
  hydrogen bonds       : angle       5.69258 /  4.16 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: A   70 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A  200 TYR cc_start: 0.9389 (t80) cc_final: 0.9083 (t80)
REVERT: B   48 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: B   70 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7812 (tm-30)
REVERT: B  200 TYR cc_start: 0.9397 (t80) cc_final: 0.9147 (t80)
REVERT: C   48 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: C   70 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: C  200 TYR cc_start: 0.9395 (t80) cc_final: 0.9142 (t80)
REVERT: D   48 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: D   70 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: D  200 TYR cc_start: 0.9389 (t80) cc_final: 0.9134 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 150
  average time/residue: 0.6028
  time to fit residues: 94.4723
Evaluate side-chains
  119 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain D residue  106 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 206 ASN
C 206 ASN
D 206 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.089168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.080415 restraints weight = 11546.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.93
r_work: 0.3019 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6412  Z= 0.155
  Angle     :  0.519   4.995   8724  Z= 0.278
  Chirality :  0.040   0.121    904
  Planarity :  0.004   0.038   1140
  Dihedral  :  7.112  83.806    844
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 10.92 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.10 (0.30), residues: 784
  helix:  0.86 (0.22), residues: 508
  sheet:  1.74 (0.63), residues: 72
  loop :  0.33 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 216 
 TYR   0.009   0.001   TYR A  33 
 PHE   0.006   0.001   PHE D 101 
 TRP   0.008   0.001   TRP B 147 
 HIS   0.003   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 ( 6412)
  covalent geometry    : angle       0.51945 /  0.28 ( 8724)
  hydrogen bonds       : bond        0.04089 /  2.75 (  404)
  hydrogen bonds       : angle       5.60101 /  4.12 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8545 (tm-30)
REVERT: A   70 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8002 (tm-30)
REVERT: A  200 TYR cc_start: 0.9571 (t80) cc_final: 0.9309 (t80)
REVERT: B   48 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8544 (tm-30)
REVERT: B   70 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: B  200 TYR cc_start: 0.9570 (t80) cc_final: 0.9312 (t80)
REVERT: B  218 MET cc_start: 0.8520 (tpp) cc_final: 0.8306 (mpp)
REVERT: C   48 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: C   70 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8018 (tm-30)
REVERT: C  200 TYR cc_start: 0.9571 (t80) cc_final: 0.9309 (t80)
REVERT: C  218 MET cc_start: 0.8493 (tpp) cc_final: 0.8275 (mpp)
REVERT: D   48 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8546 (tm-30)
REVERT: D   70 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: D  200 TYR cc_start: 0.9572 (t80) cc_final: 0.9357 (t80)
REVERT: D  218 MET cc_start: 0.8481 (tpp) cc_final: 0.8260 (mpp)
  outliers start: 16
  outliers final: 4
  residues processed: 118
  average time/residue: 0.6028
  time to fit residues: 74.4341
Evaluate side-chains
  105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain D residue  106 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0060
   chunk 53 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.5798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 206 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.089247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.079441 restraints weight = 11298.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.15
r_work: 0.2966 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6412  Z= 0.131
  Angle     :  0.507   4.950   8724  Z= 0.272
  Chirality :  0.039   0.122    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.076  83.461    844
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 11.55 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.05 (0.29), residues: 784
  helix:  0.81 (0.22), residues: 508
  sheet:  1.57 (0.59), residues: 80
  loop :  0.33 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 197 
 TYR   0.008   0.001   TYR A  33 
 PHE   0.005   0.001   PHE C 101 
 TRP   0.007   0.001   TRP A 147 
 HIS   0.002   0.001   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 6412)
  covalent geometry    : angle       0.50744 /  0.27 ( 8724)
  hydrogen bonds       : bond        0.03758 /  2.53 (  404)
  hydrogen bonds       : angle       5.37339 /  3.96 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8090 (tm-30)
REVERT: A   70 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: A  200 TYR cc_start: 0.9424 (t80) cc_final: 0.9138 (t80)
REVERT: A  218 MET cc_start: 0.7951 (tpp) cc_final: 0.7639 (mpp)
REVERT: B   48 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: B   70 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7691 (tm-30)
REVERT: B  119 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8443 (mp0)
REVERT: B  200 TYR cc_start: 0.9423 (t80) cc_final: 0.9138 (t80)
REVERT: C   48 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8087 (tm-30)
REVERT: C   70 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: C  119 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8468 (mp0)
REVERT: C  200 TYR cc_start: 0.9426 (t80) cc_final: 0.9137 (t80)
REVERT: D   48 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: D   70 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: D  119 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8468 (mp0)
REVERT: D  200 TYR cc_start: 0.9423 (t80) cc_final: 0.9134 (t80)
  outliers start: 24
  outliers final: 19
  residues processed: 138
  average time/residue: 0.4818
  time to fit residues: 70.0898
Evaluate side-chains
  123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Chi-restraints excluded: chain D residue  199 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.088630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.079826 restraints weight = 11785.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.93
r_work: 0.3007 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   6412  Z= 0.162
  Angle     :  0.522   5.051   8724  Z= 0.279
  Chirality :  0.040   0.124    904
  Planarity :  0.004   0.036   1140
  Dihedral  :  7.053  82.840    844
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 12.34 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.03 (0.29), residues: 784
  helix:  0.82 (0.22), residues: 508
  sheet:  1.63 (0.64), residues: 72
  loop :  0.28 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 197 
 TYR   0.009   0.001   TYR A  33 
 PHE   0.006   0.001   PHE D 101 
 TRP   0.007   0.001   TRP B 147 
 HIS   0.003   0.001   HIS C  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 6412)
  covalent geometry    : angle       0.52244 /  0.28 ( 8724)
  hydrogen bonds       : bond        0.03973 /  2.67 (  404)
  hydrogen bonds       : angle       5.51223 /  4.07 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: B   70 GLN cc_start: 0.8508 (tm-30) cc_final: 0.7971 (tm-30)
REVERT: B  200 TYR cc_start: 0.9577 (t80) cc_final: 0.9333 (t80)
REVERT: B  218 MET cc_start: 0.8575 (tpp) cc_final: 0.8244 (mpp)
REVERT: C   70 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7996 (tm-30)
REVERT: C  218 MET cc_start: 0.8577 (tpp) cc_final: 0.8243 (mpp)
REVERT: D   70 GLN cc_start: 0.8508 (tm-30) cc_final: 0.7978 (tm-30)
REVERT: D  218 MET cc_start: 0.8565 (tpp) cc_final: 0.8232 (mpp)
  outliers start: 24
  outliers final: 19
  residues processed: 116
  average time/residue: 0.5257
  time to fit residues: 63.8057
Evaluate side-chains
  119 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.5588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.084638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.075555 restraints weight = 11719.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.95
r_work: 0.2880 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   6412  Z= 0.252
  Angle     :  0.594   5.210   8724  Z= 0.316
  Chirality :  0.042   0.123    904
  Planarity :  0.004   0.036   1140
  Dihedral  :  7.066  81.175    844
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.92 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.80 (0.30), residues: 784
  helix:  0.69 (0.22), residues: 508
  sheet:  1.47 (0.66), residues: 72
  loop :  0.07 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 197 
 TYR   0.013   0.002   TYR C  33 
 PHE   0.007   0.001   PHE D 101 
 TRP   0.008   0.002   TRP D 147 
 HIS   0.004   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00591 /  0.25 ( 6412)
  covalent geometry    : angle       0.59401 /  0.32 ( 8724)
  hydrogen bonds       : bond        0.04485 /  3.05 (  404)
  hydrogen bonds       : angle       5.79591 /  4.28 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7720 (tm-30)
REVERT: A  218 MET cc_start: 0.8045 (tpp) cc_final: 0.7763 (mpp)
REVERT: B   70 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7708 (tm-30)
REVERT: B  200 TYR cc_start: 0.9422 (t80) cc_final: 0.9186 (t80)
REVERT: C   70 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: D   70 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7743 (tm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 119
  average time/residue: 0.5300
  time to fit residues: 66.2688
Evaluate side-chains
  116 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 158 HIS
C 160 GLN
D 158 HIS
D 160 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.086524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.076236 restraints weight = 11628.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.33
r_work: 0.2895 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6412  Z= 0.155
  Angle     :  0.547   5.421   8724  Z= 0.292
  Chirality :  0.040   0.122    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.040  82.126    844
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.24 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.88 (0.30), residues: 784
  helix:  0.83 (0.23), residues: 504
  sheet:  1.29 (0.64), residues: 72
  loop : -0.02 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 197 
 TYR   0.010   0.001   TYR C 200 
 PHE   0.005   0.001   PHE B 101 
 TRP   0.009   0.001   TRP D 147 
 HIS   0.003   0.001   HIS C  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 6412)
  covalent geometry    : angle       0.54698 /  0.29 ( 8724)
  hydrogen bonds       : bond        0.03918 /  2.64 (  404)
  hydrogen bonds       : angle       5.49398 /  4.06 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: A  218 MET cc_start: 0.7972 (tpp) cc_final: 0.7631 (mpp)
REVERT: B   70 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7682 (tm-30)
REVERT: B  200 TYR cc_start: 0.9428 (t80) cc_final: 0.9195 (t80)
REVERT: B  218 MET cc_start: 0.8041 (tpp) cc_final: 0.7635 (mpp)
REVERT: C   70 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: C  218 MET cc_start: 0.8033 (tpp) cc_final: 0.7627 (mpp)
REVERT: D   70 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: D  218 MET cc_start: 0.8038 (tpp) cc_final: 0.7632 (mpp)
  outliers start: 19
  outliers final: 16
  residues processed: 115
  average time/residue: 0.5683
  time to fit residues: 68.4201
Evaluate side-chains
  116 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.087846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.077472 restraints weight = 11704.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.25
r_work: 0.2883 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6412  Z= 0.163
  Angle     :  0.549   5.086   8724  Z= 0.293
  Chirality :  0.040   0.119    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.065  82.568    844
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.56 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.85 (0.29), residues: 784
  helix:  0.82 (0.22), residues: 504
  sheet:  1.25 (0.64), residues: 72
  loop : -0.05 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 197 
 TYR   0.009   0.001   TYR B  33 
 PHE   0.005   0.001   PHE B 101 
 TRP   0.008   0.001   TRP C 147 
 HIS   0.004   0.001   HIS D 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.16 ( 6412)
  covalent geometry    : angle       0.54946 /  0.29 ( 8724)
  hydrogen bonds       : bond        0.03941 /  2.66 (  404)
  hydrogen bonds       : angle       5.49266 /  4.06 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: A  200 TYR cc_start: 0.9393 (t80) cc_final: 0.9160 (t80)
REVERT: A  211 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7991 (tp30)
REVERT: A  218 MET cc_start: 0.8030 (tpp) cc_final: 0.7718 (mpp)
REVERT: B   70 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: B  119 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8435 (mp0)
REVERT: B  200 TYR cc_start: 0.9376 (t80) cc_final: 0.9152 (t80)
REVERT: B  218 MET cc_start: 0.7972 (tpp) cc_final: 0.7613 (mpp)
REVERT: C   70 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7713 (tm-30)
REVERT: C  119 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8428 (mp0)
REVERT: C  200 TYR cc_start: 0.9381 (t80) cc_final: 0.9176 (t80)
REVERT: C  218 MET cc_start: 0.7960 (tpp) cc_final: 0.7604 (mpp)
REVERT: D   70 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7717 (tm-30)
REVERT: D  119 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8429 (mp0)
REVERT: D  200 TYR cc_start: 0.9396 (t80) cc_final: 0.9156 (t80)
REVERT: D  218 MET cc_start: 0.7976 (tpp) cc_final: 0.7618 (mpp)
  outliers start: 18
  outliers final: 16
  residues processed: 123
  average time/residue: 0.4787
  time to fit residues: 61.7526
Evaluate side-chains
  116 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0070
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5398

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.081078 restraints weight = 11708.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.99
r_work: 0.3023 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6412  Z= 0.130
  Angle     :  0.534   6.212   8724  Z= 0.285
  Chirality :  0.039   0.118    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.010  83.247    844
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.46 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.94 (0.29), residues: 784
  helix:  0.90 (0.22), residues: 504
  sheet:  1.12 (0.64), residues: 72
  loop :  0.01 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 156 
 TYR   0.007   0.001   TYR D  33 
 PHE   0.004   0.001   PHE B 101 
 TRP   0.008   0.001   TRP D 147 
 HIS   0.004   0.001   HIS C 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 6412)
  covalent geometry    : angle       0.53410 /  0.29 ( 8724)
  hydrogen bonds       : bond        0.03700 /  2.48 (  404)
  hydrogen bonds       : angle       5.33861 /  3.94 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8524 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: A  119 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8441 (mp0)
REVERT: A  211 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8302 (tp30)
REVERT: A  218 MET cc_start: 0.8587 (tpp) cc_final: 0.8354 (mpp)
REVERT: B   70 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7974 (tm-30)
REVERT: B  119 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8519 (mp0)
REVERT: B  177 ILE cc_start: 0.8888 (mp) cc_final: 0.8682 (mt)
REVERT: B  200 TYR cc_start: 0.9543 (t80) cc_final: 0.9333 (t80)
REVERT: B  218 MET cc_start: 0.8578 (tpp) cc_final: 0.8321 (mpp)
REVERT: C   70 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8004 (tm-30)
REVERT: C  119 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8514 (mp0)
REVERT: C  218 MET cc_start: 0.8576 (tpp) cc_final: 0.8314 (mpp)
REVERT: D   70 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7971 (tm-30)
REVERT: D  119 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8525 (mp0)
REVERT: D  200 TYR cc_start: 0.9543 (t80) cc_final: 0.9325 (t80)
REVERT: D  218 MET cc_start: 0.8573 (tpp) cc_final: 0.8310 (mpp)
  outliers start: 16
  outliers final: 17
  residues processed: 134
  average time/residue: 0.4895
  time to fit residues: 68.7842
Evaluate side-chains
  124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.088512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.079490 restraints weight = 11599.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.97
r_work: 0.2956 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6412  Z= 0.145
  Angle     :  0.543   5.019   8724  Z= 0.289
  Chirality :  0.039   0.117    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.047  83.314    844
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.61 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.97 (0.30), residues: 784
  helix:  0.92 (0.22), residues: 504
  sheet:  1.18 (0.64), residues: 72
  loop :  0.03 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 197 
 TYR   0.036   0.002   TYR A 200 
 PHE   0.005   0.001   PHE D 101 
 TRP   0.008   0.001   TRP D 147 
 HIS   0.004   0.001   HIS C 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 6412)
  covalent geometry    : angle       0.54320 /  0.29 ( 8724)
  hydrogen bonds       : bond        0.03787 /  2.54 (  404)
  hydrogen bonds       : angle       5.35830 /  3.96 ( 1164)

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: A  119 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8369 (mp0)
REVERT: A  211 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8088 (tp30)
REVERT: B   70 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: B  119 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8483 (mp0)
REVERT: B  200 TYR cc_start: 0.9414 (t80) cc_final: 0.9189 (t80)
REVERT: B  211 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8166 (tp30)
REVERT: B  218 MET cc_start: 0.8119 (tpp) cc_final: 0.7806 (mpp)
REVERT: C   70 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: C  119 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8469 (mp0)
REVERT: C  211 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8137 (tp30)
REVERT: C  218 MET cc_start: 0.8112 (tpp) cc_final: 0.7793 (mpp)
REVERT: D   70 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7810 (tm-30)
REVERT: D  119 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8483 (mp0)
REVERT: D  200 TYR cc_start: 0.9412 (t80) cc_final: 0.9179 (t80)
REVERT: D  211 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8157 (tp30)
REVERT: D  218 MET cc_start: 0.8134 (tpp) cc_final: 0.7816 (mpp)
  outliers start: 15
  outliers final: 15
  residues processed: 123
  average time/residue: 0.4896
  time to fit residues: 63.3481
Evaluate side-chains
  119 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0040
   chunk 73 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5992

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.088688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.079704 restraints weight = 11505.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.96
r_work: 0.2960 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6412  Z= 0.134
  Angle     :  0.521   5.001   8724  Z= 0.277
  Chirality :  0.039   0.118    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.015  82.931    844
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.51 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  1.03 (0.30), residues: 784
  helix:  0.97 (0.22), residues: 504
  sheet:  1.15 (0.64), residues: 72
  loop :  0.05 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 156 
 TYR   0.008   0.001   TYR C 200 
 PHE   0.004   0.001   PHE D 101 
 TRP   0.008   0.001   TRP D 147 
 HIS   0.004   0.001   HIS C 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 6412)
  covalent geometry    : angle       0.52142 /  0.28 ( 8724)
  hydrogen bonds       : bond        0.03748 /  2.51 (  404)
  hydrogen bonds       : angle       5.33671 /  3.94 ( 1164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2022.01 seconds
wall clock time: 35 minutes 24.08 seconds (2124.08 seconds total)