Starting phenix.real_space_refine
on Wed Jun  3 21:20:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9px6_71953/06_2026/9px6_71953.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9px6_71953/06_2026/9px6_71953.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9px6_71953/06_2026/9px6_71953.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9px6_71953/06_2026/9px6_71953.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9px6_71953/06_2026/9px6_71953.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9px6_71953/06_2026/9px6_71953.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.020
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
     S       6      5.16       5
     C    2778      2.51       5
     N     702      2.21       5
     O     798      1.98       5
     H    4296      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8580
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1430
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.36, per 1000 atoms: 0.16
  Number of scatterers: 8580
  At special positions: 0
  Unit cell: (76.14, 88.36, 47.94, 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       6     16.00
     O     798      8.00
     N     702      7.00
     C    2778      6.00
     H    4296      1.00
    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: 0.76
  Conformation dependent library (CDL) restraints added in 209.1 milliseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1044

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 48.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21
    Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34
      removed outlier: 6.521A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   VAL B  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ASN A  27 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   VAL B  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ALA A  29 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   VAL B  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.238A  pdb=" N   ARG B  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE A  33 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ALA B  25 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   VAL C  28 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASN B  27 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   VAL C  30 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ALA B  29 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   VAL C  32 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   HIS B  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   ARG C  34 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   PHE B  33 " --> pdb=" O   ARG C  34 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA C  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   VAL D  28 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASN C  27 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   VAL D  30 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ALA C  29 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   VAL D  32 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   HIS C  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   ARG D  34 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   PHE C  33 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA D  25 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   VAL E  28 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ASN D  27 " --> pdb=" O   VAL E  28 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   VAL E  30 " --> pdb=" O   ASN D  27 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA D  29 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   VAL E  32 " --> pdb=" O   ALA D  29 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   HIS D  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   ARG E  34 " --> pdb=" O   HIS D  31 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   PHE D  33 " --> pdb=" O   ARG E  34 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA E  25 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   VAL F  28 " --> pdb=" O   ALA E  25 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ASN E  27 " --> pdb=" O   VAL F  28 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   VAL F  30 " --> pdb=" O   ASN E  27 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ALA E  29 " --> pdb=" O   VAL F  30 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   VAL F  32 " --> pdb=" O   ALA E  29 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   HIS E  31 " --> pdb=" O   VAL F  32 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   ARG F  34 " --> pdb=" O   HIS E  31 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   PHE E  33 " --> pdb=" O   ARG F  34 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 65
      removed outlier: 6.911A  pdb=" N   PHE A  64 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL B  65 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   PHE B  64 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL C  65 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   PHE C  64 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL D  65 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   PHE D  64 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   VAL E  65 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   PHE E  64 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   VAL F  65 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 68 through 79
      removed outlier: 6.995A  pdb=" N   TYR A  69 " --> pdb=" O   ILE B  68 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ASP B  74 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   THR A  75 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   LYS B  76 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   SER A  77 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   TYR B  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   TYR B  69 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASP C  74 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   THR B  75 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   LYS C  76 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   SER B  77 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   TYR C  78 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   TYR C  69 " --> pdb=" O   ILE D  68 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASP D  74 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   THR C  75 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   LYS D  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   SER C  77 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   TYR D  78 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   TYR D  69 " --> pdb=" O   ILE E  68 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASP E  74 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR D  75 " --> pdb=" O   ASP E  74 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   LYS E  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   SER D  77 " --> pdb=" O   LYS E  76 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   TYR E  78 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   TYR E  69 " --> pdb=" O   ILE F  68 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   ASP F  74 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   THR E  75 " --> pdb=" O   ASP F  74 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LYS F  76 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   SER E  77 " --> pdb=" O   LYS F  76 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   TYR F  78 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 97
    Processing sheet with id=AA7, first strand: chain 'A' and resid 103 through 110
      removed outlier: 6.964A  pdb=" N   ALA A 109 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU B 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ALA B 109 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   LEU C 110 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ALA C 109 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU D 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ALA D 109 " --> pdb=" O   ALA E 108 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU E 110 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ARG E 103 " --> pdb=" O   ARG F 104 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   THR F 106 " --> pdb=" O   ARG E 103 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   TYR E 105 " --> pdb=" O   THR F 106 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   ALA F 108 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 9.061A  pdb=" N   ILE E 107 " --> pdb=" O   ALA F 108 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   LEU F 110 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 9.012A  pdb=" N   ALA E 109 " --> pdb=" O   LEU F 110 " (cutoff:3.500A)

    120 hydrogen bonds defined for protein.
    360 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: 2.01

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4296
        1.03 -     1.22: 0
        1.22 -     1.42: 1836
        1.42 -     1.61: 2538
        1.61 -     1.81: 12
  Bond restraints: 8682
  Sorted by residual:
  bond pdb=" CG  LEU C 110 "
       pdb=" CD1 LEU C 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.37e+00
  bond pdb=" CG  LEU B 110 "
       pdb=" CD1 LEU B 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.36e+00
  bond pdb=" CG  LEU D 110 "
       pdb=" CD1 LEU D 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.36e+00
  bond pdb=" CG  LEU F 110 "
       pdb=" CD1 LEU F 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.35e+00
  bond pdb=" CG  LEU A 110 "
       pdb=" CD1 LEU A 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.34e+00
  ... (remaining 8677 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 15505
        1.60 -     3.20: 167
        3.20 -     4.80: 24
        4.80 -     6.40: 0
        6.40 -     8.00: 6
  Bond angle restraints: 15702
  Sorted by residual:
  angle pdb=" CA  GLU A  66 "
        pdb=" CB  GLU A  66 "
        pdb=" CG  GLU A  66 "
      ideal   model   delta    sigma   weight residual
     114.10  122.10   -8.00 2.00e+00 2.50e-01 1.60e+01
  angle pdb=" CA  GLU F  66 "
        pdb=" CB  GLU F  66 "
        pdb=" CG  GLU F  66 "
      ideal   model   delta    sigma   weight residual
     114.10  122.09   -7.99 2.00e+00 2.50e-01 1.59e+01
  angle pdb=" CA  GLU C  66 "
        pdb=" CB  GLU C  66 "
        pdb=" CG  GLU C  66 "
      ideal   model   delta    sigma   weight residual
     114.10  122.08   -7.98 2.00e+00 2.50e-01 1.59e+01
  angle pdb=" CA  GLU E  66 "
        pdb=" CB  GLU E  66 "
        pdb=" CG  GLU E  66 "
      ideal   model   delta    sigma   weight residual
     114.10  122.07   -7.97 2.00e+00 2.50e-01 1.59e+01
  angle pdb=" CA  GLU D  66 "
        pdb=" CB  GLU D  66 "
        pdb=" CG  GLU D  66 "
      ideal   model   delta    sigma   weight residual
     114.10  122.05   -7.95 2.00e+00 2.50e-01 1.58e+01
  ... (remaining 15697 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 3672
       17.55 -    35.11: 312
       35.11 -    52.66: 120
       52.66 -    70.22: 6
       70.22 -    87.77: 12
  Dihedral angle restraints: 4122
    sinusoidal: 2184
      harmonic: 1938
  Sorted by residual:
  dihedral pdb=" CA  VAL C  65 "
           pdb=" C   VAL C  65 "
           pdb=" N   GLU C  66 "
           pdb=" CA  GLU C  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.26  -23.74     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  VAL F  65 "
           pdb=" C   VAL F  65 "
           pdb=" N   GLU F  66 "
           pdb=" CA  GLU F  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.27  -23.73     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  VAL B  65 "
           pdb=" C   VAL B  65 "
           pdb=" N   GLU B  66 "
           pdb=" CA  GLU B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.29  -23.71     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 4119 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 352
       0.027 -    0.054: 179
       0.054 -    0.081: 69
       0.081 -    0.108: 61
       0.108 -    0.135: 47
  Chirality restraints: 708
  Sorted by residual:
  chirality pdb=" CA  PRO D  86 "
            pdb=" N   PRO D  86 "
            pdb=" C   PRO D  86 "
            pdb=" CB  PRO D  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  PRO F  86 "
            pdb=" N   PRO F  86 "
            pdb=" C   PRO F  86 "
            pdb=" CB  PRO F  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" CA  PRO B  86 "
            pdb=" N   PRO B  86 "
            pdb=" C   PRO B  86 "
            pdb=" CB  PRO B  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.56e-01
  ... (remaining 705 not shown)

  Planarity restraints: 1242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  69 "    0.014 2.00e-02 2.50e+03   8.28e-03 2.05e+00
        pdb=" CG  TYR B  69 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  69 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  69 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  69 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  69 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD1 TYR B  69 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR B  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR B  69 "    0.000 2.00e-02 2.50e+03
        pdb=" HE2 TYR B  69 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F  85 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO F  86 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO F  86 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F  86 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  85 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO C  86 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO C  86 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C  86 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1239 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.39: 3829
        2.39 -     2.94: 19824
        2.94 -     3.50: 22015
        3.50 -     4.05: 32050
        4.05 -     4.60: 44623
  Nonbonded interactions: 122341
  Sorted by model distance:
  nonbonded pdb=" HE1 TYR E 116 "
            pdb=" HG  SER F  23 "
     model   vdw
     1.838 2.100
  nonbonded pdb=" HE1 TYR B 116 "
            pdb=" HG  SER C  23 "
     model   vdw
     1.895 2.100
  nonbonded pdb=" HE1 TYR D 116 "
            pdb=" HG  SER E  23 "
     model   vdw
     1.900 2.100
  nonbonded pdb=" HE1 TYR A 116 "
            pdb=" HG  SER B  23 "
     model   vdw
     1.916 2.100
  nonbonded pdb=" HE1 TYR C 116 "
            pdb=" HG  SER D  23 "
     model   vdw
     1.926 2.100
  ... (remaining 122336 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'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.040
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.700
  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:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4386  Z= 0.148
  Angle     :  0.618   8.005   5970  Z= 0.347
  Chirality :  0.051   0.135    708
  Planarity :  0.005   0.036    732
  Dihedral  : 14.887  79.789   1548
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.54 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.34), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 103 
 TYR   0.024   0.002   TYR C  69 
 PHE   0.004   0.001   PHE C  95 
 TRP   0.001   0.001   TRP F  79 
 HIS   0.002   0.001   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 ( 4386)
  covalent geometry    : angle       0.61790 /  0.35 ( 5970)
  hydrogen bonds       : bond        0.19402 / 13.84 (  120)
  hydrogen bonds       : angle       7.10356 /  4.95 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLU cc_start: 0.8086 (pp20) cc_final: 0.7741 (mm-30)
REVERT: A   70 LYS cc_start: 0.8738 (tttt) cc_final: 0.8114 (pttm)
REVERT: A   80 LYS cc_start: 0.8811 (tptm) cc_final: 0.7888 (pttm)
REVERT: B   89 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8279 (mp0)
REVERT: F   15 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7475 (pttm)
REVERT: F   70 LYS cc_start: 0.8853 (tttt) cc_final: 0.8571 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1957
  time to fit residues: 30.1714
Evaluate side-chains
  98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    3.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.113080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.105941 restraints weight = 30882.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.4289 rms_B_bonded: 3.25
r_work: 0.4193 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
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   0.031   4386  Z= 0.179
  Angle     :  0.564   3.945   5970  Z= 0.310
  Chirality :  0.050   0.140    708
  Planarity :  0.005   0.036    732
  Dihedral  :  5.849  18.233    588
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 12.82 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.34), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  21 
 TYR   0.008   0.001   TYR C  78 
 PHE   0.009   0.001   PHE B  33 
 TRP   0.004   0.001   TRP C  79 
 HIS   0.002   0.001   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.18 ( 4386)
  covalent geometry    : angle       0.56392 /  0.31 ( 5970)
  hydrogen bonds       : bond        0.05185 /  3.69 (  120)
  hydrogen bonds       : angle       6.06539 /  4.22 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8387 (tttt) cc_final: 0.7686 (pttm)
REVERT: A   80 LYS cc_start: 0.8595 (tptm) cc_final: 0.7347 (pttm)
REVERT: C   66 GLU cc_start: 0.8256 (tp30) cc_final: 0.7819 (tp30)
REVERT: D   15 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7334 (mtpt)
REVERT: D   62 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7249 (pp20)
REVERT: D   66 GLU cc_start: 0.8366 (tp30) cc_final: 0.8003 (tp30)
REVERT: E   61 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8686 (mt-10)
REVERT: E   80 LYS cc_start: 0.8645 (tptp) cc_final: 0.8398 (tptm)
REVERT: F   70 LYS cc_start: 0.7979 (tttt) cc_final: 0.7488 (tppt)
REVERT: F   99 ASP cc_start: 0.7967 (p0) cc_final: 0.7752 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1663
  time to fit residues: 21.7063
Evaluate side-chains
  102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   62 GLU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    2.1388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.111720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.104333 restraints weight = 30448.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.4252 rms_B_bonded: 3.38
r_work: 0.4157 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4386  Z= 0.136
  Angle     :  0.515   3.488   5970  Z= 0.280
  Chirality :  0.049   0.133    708
  Planarity :  0.004   0.035    732
  Dihedral  :  5.616  17.281    588
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.32 %
    Favored  : 83.12 %
  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: -2.09 (0.35), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  21 
 TYR   0.011   0.001   TYR E  69 
 PHE   0.008   0.001   PHE B  33 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.001   0.000   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 4386)
  covalent geometry    : angle       0.51524 /  0.28 ( 5970)
  hydrogen bonds       : bond        0.04177 /  2.99 (  120)
  hydrogen bonds       : angle       5.66093 /  3.93 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8335 (tttt) cc_final: 0.7672 (pttm)
REVERT: A   80 LYS cc_start: 0.8719 (tptm) cc_final: 0.7407 (pttm)
REVERT: B   72 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8900 (mt-10)
REVERT: B   92 GLU cc_start: 0.7906 (mp0) cc_final: 0.7539 (mp0)
REVERT: C   66 GLU cc_start: 0.8137 (tp30) cc_final: 0.7661 (tp30)
REVERT: D   15 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7275 (mtpt)
REVERT: D   62 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7193 (pp20)
REVERT: E   80 LYS cc_start: 0.8632 (tptp) cc_final: 0.8369 (tptm)
REVERT: F   61 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7864 (mt-10)
REVERT: F   70 LYS cc_start: 0.7924 (tttt) cc_final: 0.7392 (tppt)
REVERT: F   99 ASP cc_start: 0.7815 (p0) cc_final: 0.7592 (t70)
  outliers start: 12
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1624
  time to fit residues: 20.4733
Evaluate side-chains
  102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue   62 GLU
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.116250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.108313 restraints weight = 30627.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.4284 rms_B_bonded: 3.37
r_work: 0.4195 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4386  Z= 0.124
  Angle     :  0.510   3.859   5970  Z= 0.276
  Chirality :  0.049   0.131    708
  Planarity :  0.004   0.035    732
  Dihedral  :  5.494  17.128    588
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.38 %
    Favored  : 81.84 %
  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: -2.07 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.57 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  21 
 TYR   0.009   0.001   TYR E  69 
 PHE   0.007   0.001   PHE B  95 
 TRP   0.001   0.000   TRP A  79 
 HIS   0.001   0.000   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 4386)
  covalent geometry    : angle       0.50978 /  0.28 ( 5970)
  hydrogen bonds       : bond        0.03610 /  2.59 (  120)
  hydrogen bonds       : angle       5.47943 /  3.80 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8468 (tttt) cc_final: 0.7732 (pttm)
REVERT: A   80 LYS cc_start: 0.8666 (tptm) cc_final: 0.7323 (pttm)
REVERT: B   92 GLU cc_start: 0.7936 (mp0) cc_final: 0.7447 (mp0)
REVERT: C   66 GLU cc_start: 0.8038 (tp30) cc_final: 0.7617 (tp30)
REVERT: D   15 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7310 (mtpt)
REVERT: D   62 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7226 (pp20)
REVERT: F   70 LYS cc_start: 0.7722 (tttt) cc_final: 0.7164 (tppt)
REVERT: F   99 ASP cc_start: 0.7670 (p0) cc_final: 0.7451 (t70)
  outliers start: 13
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1775
  time to fit residues: 22.3004
Evaluate side-chains
  104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue   62 GLU
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.110824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.103620 restraints weight = 29913.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 3.31
r_work: 0.4020 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4386  Z= 0.230
  Angle     :  0.558   3.903   5970  Z= 0.306
  Chirality :  0.048   0.143    708
  Planarity :  0.004   0.038    732
  Dihedral  :  5.698  18.146    588
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.54 %
    Favored  : 89.46 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.38 %
    Favored  : 81.84 %
  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: -2.24 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  21 
 TYR   0.010   0.001   TYR E  69 
 PHE   0.009   0.002   PHE B  95 
 TRP   0.003   0.001   TRP F  79 
 HIS   0.003   0.001   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.23 ( 4386)
  covalent geometry    : angle       0.55846 /  0.31 ( 5970)
  hydrogen bonds       : bond        0.04345 /  3.10 (  120)
  hydrogen bonds       : angle       5.75483 /  3.98 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8095 (tt0) cc_final: 0.7519 (tt0)
REVERT: A   70 LYS cc_start: 0.8449 (tttt) cc_final: 0.7630 (pttm)
REVERT: A   80 LYS cc_start: 0.8557 (tptm) cc_final: 0.7239 (pttm)
REVERT: B   63 GLU cc_start: 0.8968 (tt0) cc_final: 0.8619 (tt0)
REVERT: B   92 GLU cc_start: 0.8124 (mp0) cc_final: 0.7590 (mp0)
REVERT: C   66 GLU cc_start: 0.8160 (tp30) cc_final: 0.7711 (tp30)
REVERT: C   92 GLU cc_start: 0.6901 (mp0) cc_final: 0.6561 (mp0)
REVERT: D   15 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7428 (mtpt)
REVERT: E   66 GLU cc_start: 0.8068 (tp30) cc_final: 0.7657 (tp30)
REVERT: F   70 LYS cc_start: 0.7667 (tttt) cc_final: 0.7138 (tppt)
  outliers start: 13
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1611
  time to fit residues: 18.4848
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.118463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.110486 restraints weight = 28969.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 3.24
r_work: 0.4076 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4386  Z= 0.193
  Angle     :  0.531   3.462   5970  Z= 0.291
  Chirality :  0.049   0.139    708
  Planarity :  0.004   0.036    732
  Dihedral  :  5.694  18.187    588
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.81 %
    Favored  : 81.62 %
  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: -2.27 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 103 
 TYR   0.010   0.001   TYR E  78 
 PHE   0.008   0.001   PHE B  95 
 TRP   0.003   0.001   TRP F  79 
 HIS   0.003   0.001   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.19 ( 4386)
  covalent geometry    : angle       0.53137 /  0.29 ( 5970)
  hydrogen bonds       : bond        0.03928 /  2.81 (  120)
  hydrogen bonds       : angle       5.59367 /  3.88 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8057 (tt0) cc_final: 0.7618 (tt0)
REVERT: A   70 LYS cc_start: 0.8464 (tttt) cc_final: 0.7640 (pttm)
REVERT: A   80 LYS cc_start: 0.8579 (tptm) cc_final: 0.7215 (pttm)
REVERT: B   63 GLU cc_start: 0.8995 (tt0) cc_final: 0.8741 (tt0)
REVERT: B   92 GLU cc_start: 0.8086 (mp0) cc_final: 0.7581 (mp0)
REVERT: C   66 GLU cc_start: 0.8166 (tp30) cc_final: 0.7729 (tp30)
REVERT: C   92 GLU cc_start: 0.6886 (mp0) cc_final: 0.6548 (mp0)
REVERT: D   15 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7769 (mttm)
REVERT: D   18 ASP cc_start: 0.8753 (t0) cc_final: 0.8493 (m-30)
REVERT: E   18 ASP cc_start: 0.8675 (t0) cc_final: 0.8390 (m-30)
REVERT: F   70 LYS cc_start: 0.7544 (tttt) cc_final: 0.7035 (tppt)
  outliers start: 12
  outliers final: 9
  residues processed: 96
  average time/residue: 0.1548
  time to fit residues: 19.1064
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.0570
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.3102

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.122598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.114485 restraints weight = 28851.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 3.25
r_work: 0.4145 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4386  Z= 0.104
  Angle     :  0.511   4.518   5970  Z= 0.274
  Chirality :  0.050   0.129    708
  Planarity :  0.004   0.034    732
  Dihedral  :  5.435  17.269    588
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.45 %
    Favored  : 81.20 %
  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: -2.20 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  21 
 TYR   0.009   0.001   TYR E  78 
 PHE   0.006   0.001   PHE C  95 
 TRP   0.001   0.000   TRP F  79 
 HIS   0.001   0.000   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.10 ( 4386)
  covalent geometry    : angle       0.51117 /  0.27 ( 5970)
  hydrogen bonds       : bond        0.03248 /  2.31 (  120)
  hydrogen bonds       : angle       5.16557 /  3.58 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8461 (tttt) cc_final: 0.7720 (pttm)
REVERT: A   80 LYS cc_start: 0.8599 (tptm) cc_final: 0.7270 (pttm)
REVERT: B   66 GLU cc_start: 0.7804 (tp30) cc_final: 0.7298 (tp30)
REVERT: B   92 GLU cc_start: 0.8107 (mp0) cc_final: 0.7608 (mp0)
REVERT: C   92 GLU cc_start: 0.6937 (mp0) cc_final: 0.6727 (mp0)
REVERT: E   18 ASP cc_start: 0.8586 (t0) cc_final: 0.8230 (m-30)
REVERT: F   70 LYS cc_start: 0.7412 (tttt) cc_final: 0.6947 (tppt)
  outliers start: 11
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1510
  time to fit residues: 19.0423
Evaluate side-chains
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.116907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.109035 restraints weight = 29304.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 3.15
r_work: 0.4088 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   4386  Z= 0.247
  Angle     :  0.566   6.821   5970  Z= 0.308
  Chirality :  0.049   0.144    708
  Planarity :  0.004   0.038    732
  Dihedral  :  5.643  18.142    588
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.73 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.03 %
    Favored  : 81.62 %
  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: -2.34 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 103 
 TYR   0.010   0.001   TYR E  69 
 PHE   0.009   0.001   PHE B  95 
 TRP   0.004   0.001   TRP F  79 
 HIS   0.003   0.001   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00573 /  0.25 ( 4386)
  covalent geometry    : angle       0.56583 /  0.31 ( 5970)
  hydrogen bonds       : bond        0.04056 /  2.89 (  120)
  hydrogen bonds       : angle       5.62349 /  3.91 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8480 (tttt) cc_final: 0.7593 (pttm)
REVERT: A   80 LYS cc_start: 0.8490 (tptm) cc_final: 0.7129 (pttm)
REVERT: B   92 GLU cc_start: 0.8113 (mp0) cc_final: 0.7660 (mp0)
REVERT: C   66 GLU cc_start: 0.8185 (tp30) cc_final: 0.7732 (tp30)
REVERT: D   15 LYS cc_start: 0.8022 (mttt) cc_final: 0.7693 (mttp)
REVERT: F   70 LYS cc_start: 0.7634 (tttt) cc_final: 0.7139 (tppt)
  outliers start: 11
  outliers final: 11
  residues processed: 89
  average time/residue: 0.1561
  time to fit residues: 17.7688
Evaluate side-chains
  93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.114283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.106887 restraints weight = 28712.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 3.27
r_work: 0.4074 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4386  Z= 0.175
  Angle     :  0.538   4.539   5970  Z= 0.293
  Chirality :  0.049   0.136    708
  Planarity :  0.004   0.035    732
  Dihedral  :  5.622  17.978    588
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.74 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 103 
 TYR   0.010   0.001   TYR E  78 
 PHE   0.007   0.001   PHE B  95 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.002   0.000   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.18 ( 4386)
  covalent geometry    : angle       0.53802 /  0.29 ( 5970)
  hydrogen bonds       : bond        0.03768 /  2.70 (  120)
  hydrogen bonds       : angle       5.46311 /  3.80 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.8449 (tttt) cc_final: 0.7619 (pttm)
REVERT: A   80 LYS cc_start: 0.8503 (tptm) cc_final: 0.7179 (pttm)
REVERT: B   66 GLU cc_start: 0.7871 (tp30) cc_final: 0.7478 (tp30)
REVERT: B   92 GLU cc_start: 0.8150 (mp0) cc_final: 0.7712 (mp0)
REVERT: C   66 GLU cc_start: 0.8110 (tp30) cc_final: 0.7556 (tp30)
REVERT: D   15 LYS cc_start: 0.8008 (mttt) cc_final: 0.7595 (mttp)
REVERT: D   92 GLU cc_start: 0.7839 (mp0) cc_final: 0.7485 (mp0)
REVERT: F   70 LYS cc_start: 0.7480 (tttt) cc_final: 0.7040 (tppt)
  outliers start: 9
  outliers final: 9
  residues processed: 91
  average time/residue: 0.1504
  time to fit residues: 17.4548
Evaluate side-chains
  93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.111474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.104157 restraints weight = 29453.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 3.24
r_work: 0.4063 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4386  Z= 0.187
  Angle     :  0.535   3.489   5970  Z= 0.292
  Chirality :  0.049   0.139    708
  Planarity :  0.004   0.037    732
  Dihedral  :  5.608  18.015    588
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.09 %
    Favored  : 80.77 %
  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: -2.33 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 103 
 TYR   0.010   0.001   TYR D  69 
 PHE   0.008   0.001   PHE B  95 
 TRP   0.003   0.001   TRP A  79 
 HIS   0.002   0.001   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.19 ( 4386)
  covalent geometry    : angle       0.53485 /  0.29 ( 5970)
  hydrogen bonds       : bond        0.03800 /  2.71 (  120)
  hydrogen bonds       : angle       5.47474 /  3.80 (  360)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.8379 (tt0) cc_final: 0.7845 (tt0)
REVERT: A   70 LYS cc_start: 0.8456 (tttt) cc_final: 0.7579 (pttm)
REVERT: A   80 LYS cc_start: 0.8527 (tptm) cc_final: 0.7208 (pttm)
REVERT: B   66 GLU cc_start: 0.7881 (tp30) cc_final: 0.7487 (tp30)
REVERT: B   92 GLU cc_start: 0.8237 (mp0) cc_final: 0.7726 (mp0)
REVERT: C   66 GLU cc_start: 0.8132 (tp30) cc_final: 0.7571 (tp30)
REVERT: D   15 LYS cc_start: 0.8011 (mttt) cc_final: 0.7511 (mttm)
REVERT: F   70 LYS cc_start: 0.7476 (tttt) cc_final: 0.7021 (tppt)
  outliers start: 10
  outliers final: 10
  residues processed: 87
  average time/residue: 0.1452
  time to fit residues: 16.3167
Evaluate side-chains
  91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.115645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.108137 restraints weight = 28311.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.4162 rms_B_bonded: 3.29
r_work: 0.4079 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4386  Z= 0.138
  Angle     :  0.516   3.387   5970  Z= 0.280
  Chirality :  0.049   0.130    708
  Planarity :  0.004   0.035    732
  Dihedral  :  5.524  17.573    588
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.88 %
    Favored  : 80.77 %
  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: -2.29 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 103 
 TYR   0.010   0.001   TYR D  69 
 PHE   0.007   0.001   PHE B  95 
 TRP   0.002   0.001   TRP E  79 
 HIS   0.002   0.000   HIS F  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 4386)
  covalent geometry    : angle       0.51568 /  0.28 ( 5970)
  hydrogen bonds       : bond        0.03455 /  2.47 (  120)
  hydrogen bonds       : angle       5.25918 /  3.65 (  360)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2394.43 seconds
wall clock time: 41 minutes 21.49 seconds (2481.49 seconds total)