Starting phenix.real_space_refine
on Fri Jul  3 10:21:17 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2026/8smz_40607.map"
  }
  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=   0.000 sd=   0.105
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7891      2.51       5
     N    2608      2.21       5
     O    3171      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: 13998
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      34.493  67.206  42.369  1.00 54.60           S
  ATOM  12446  SG  CYS K  51      32.878  63.788  42.788  1.00 53.45           S
  ATOM  12470  SG  CYS K  54      34.673  64.732  39.472  1.00 59.59           S
  ATOM  12187  SG  CYS K  16      22.650  64.083  47.853  1.00 61.09           S
  ATOM  12205  SG  CYS K  19      20.144  62.240  49.932  1.00 66.08           S
  ATOM  12335  SG  CYS K  36      22.147  65.128  51.321  1.00 55.44           S
  ATOM  12357  SG  CYS K  39      23.894  61.698  50.708  1.00 56.03           S

  Time building chain proxies: 2.51, per 1000 atoms: 0.18
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 128.816, 127.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2608      7.00
     C    7891      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 483.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
      Number of angles added : 9


  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 11 sheets defined
      64.8% alpha, 4.2% beta
      136 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 2.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.502A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.714A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.588A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.967A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.906A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.597A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.560A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.608A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.545A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.795A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.564A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.563A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.894A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
      removed outlier: 3.508A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.512A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.863A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.526A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.610A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.625A  pdb=" N   ALA G  86 " --> pdb=" O   HIS G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.541A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.592A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 4.088A  pdb=" N   THR K  62 " --> pdb=" O   VAL K  58 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ARG K  63 " --> pdb=" O   SER K  59 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.899A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.961A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS K  89 " --> pdb=" O   PRO K  85 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 4.444A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG L 125 " --> pdb=" O   PRO L 121 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.728A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.952A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.328A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.767A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.302A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.899A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24

    461 hydrogen bonds defined for protein.
    1365 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3294
        1.34 -     1.46: 4482
        1.46 -     1.58: 6455
        1.58 -     1.70: 586
        1.70 -     1.82: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.42e+01
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+01
  bond pdb=" C3'  DC I  21 "
       pdb=" C2'  DC I  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.66e+00
  bond pdb=" C3'  DT I  62 "
       pdb=" C2'  DT I  62 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.49e+00
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 19747
        1.37 -     2.74: 1480
        2.74 -     4.10: 107
        4.10 -     5.47: 13
        5.47 -     6.84: 6
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" O4'  DC J -71 "
        pdb=" C4'  DC J -71 "
        pdb=" C3'  DC J -71 "
      ideal   model   delta    sigma   weight residual
     106.00  103.12    2.88 6.00e-01 2.78e+00 2.30e+01
  angle pdb=" N3   DT J -50 "
        pdb=" C4   DT J -50 "
        pdb=" O4   DT J -50 "
      ideal   model   delta    sigma   weight residual
     119.90  122.59   -2.69 6.00e-01 2.78e+00 2.01e+01
  angle pdb=" N3   DT J -17 "
        pdb=" C4   DT J -17 "
        pdb=" O4   DT J -17 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.93e+01
  angle pdb=" N3   DT I  38 "
        pdb=" C4   DT I  38 "
        pdb=" O4   DT I  38 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.93e+01
  angle pdb=" N3   DT I  30 "
        pdb=" C4   DT I  30 "
        pdb=" O4   DT I  30 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.92e+01
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.50: 6746
       34.50 -    69.00: 1457
       69.00 -   103.50: 25
      103.50 -   138.00: 0
      138.00 -   172.50: 2
  Dihedral angle restraints: 8230
    sinusoidal: 5306
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.50  172.50     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   68.78  151.22     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" CA  ILE L  78 "
           pdb=" C   ILE L  78 "
           pdb=" N   ASN L  79 "
           pdb=" CA  ASN L  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.83   17.17     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1617
       0.042 -    0.083: 621
       0.083 -    0.125: 168
       0.125 -    0.167: 10
       0.167 -    0.208: 3
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CG  LEU L  86 "
            pdb=" CB  LEU L  86 "
            pdb=" CD1 LEU L  86 "
            pdb=" CD2 LEU L  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  ILE L 123 "
            pdb=" CA  ILE L 123 "
            pdb=" CG1 ILE L 123 "
            pdb=" CG2 ILE L 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" C3'  DT J -17 "
            pdb=" C4'  DT J -17 "
            pdb=" O3'  DT J -17 "
            pdb=" C2'  DT J -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.56   -0.17 2.00e-01 2.50e+01 7.10e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS L  75 "   -0.033 5.00e-02 4.00e+02   5.01e-02 4.02e+00
        pdb=" N   PRO L  76 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO L  76 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO L  76 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.028 2.00e-02 2.50e+03   1.15e-02 3.97e+00
        pdb=" N9   DG I  47 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.027 2.00e-02 2.50e+03   1.17e-02 3.78e+00
        pdb=" N9   DA I -35 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1902
        2.76 -     3.30: 11924
        3.30 -     3.83: 25122
        3.83 -     4.37: 31196
        4.37 -     4.90: 45644
  Nonbonded interactions: 115788
  Sorted by model distance:
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR L  45 "
            pdb=" O   TYR L  74 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" NH2 ARG K  63 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.294 2.496
  ... (remaining 115783 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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=0.17 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:             1.190
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.170
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  14874  Z= 0.492
  Angle     :  0.728   6.842  21368  Z= 0.626
  Chirality :  0.045   0.208   2419
  Planarity :  0.005   0.050   1688
  Dihedral  : 26.569 172.502   6336
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.15 (0.27), residues: 983
  helix:  1.95 (0.21), residues: 621
  sheet: -0.29 (0.99), residues: 23
  loop : -1.48 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  99 
 TYR   0.014   0.001   TYR G  50 
 PHE   0.012   0.002   PHE L  69 
 TRP   0.010   0.002   TRP L 141 
 HIS   0.003   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00565 /  0.49 (14864)
  covalent geometry    : angle       0.72528 /  0.63 (21353)
  hydrogen bonds       : bond        0.10275 /  6.78 (  810)
  hydrogen bonds       : angle       3.97434 /  2.83 ( 2059)
  metal coordination   : bond        0.02492 /  1.21 (    8)
  metal coordination   : angle       3.18961 /  1.45 (    9)
  link_TRANS           : bond        0.00115 /  0.06 (    2)
  link_TRANS           : angle       0.60516 /  0.35 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7661 (t0) cc_final: 0.7141 (t0)
REVERT: C   36 LYS cc_start: 0.8449 (mttm) cc_final: 0.8169 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1510
  time to fit residues: 22.7399
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.173791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.118703 restraints weight = 28303.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.82
r_work: 0.2904 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.2695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.0525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.172
  Angle     :  0.628   7.140  21368  Z= 0.359
  Chirality :  0.046   0.283   2419
  Planarity :  0.005   0.046   1688
  Dihedral  : 29.787 174.479   4332
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.02 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.38 (0.27), residues: 983
  helix:  2.15 (0.21), residues: 623
  sheet:  0.25 (1.09), residues: 21
  loop : -1.52 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  99 
 TYR   0.010   0.001   TYR L  45 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.004   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.17 (14864)
  covalent geometry    : angle       0.62527 /  0.36 (21353)
  hydrogen bonds       : bond        0.06483 /  4.27 (  810)
  hydrogen bonds       : angle       3.37316 /  2.40 ( 2059)
  metal coordination   : bond        0.01486 /  0.69 (    8)
  metal coordination   : angle       2.97308 /  1.33 (    9)
  link_TRANS           : bond        0.00026 /  0.01 (    2)
  link_TRANS           : angle       0.56914 /  0.28 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7773 (t0) cc_final: 0.7272 (t0)
REVERT: B   84 MET cc_start: 0.8574 (mmt) cc_final: 0.8284 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 98
  average time/residue: 0.1542
  time to fit residues: 20.4483
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   11 SER
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 117 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.171191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.117429 restraints weight = 24340.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.71
r_work: 0.2954 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.0656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14874  Z= 0.183
  Angle     :  0.619   6.374  21368  Z= 0.353
  Chirality :  0.046   0.295   2419
  Planarity :  0.005   0.048   1688
  Dihedral  : 29.897 173.981   4332
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.71 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.34 (0.27), residues: 983
  helix:  2.13 (0.21), residues: 624
  sheet:  0.28 (1.08), residues: 21
  loop : -1.55 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  92 
 TYR   0.012   0.002   TYR D 121 
 PHE   0.011   0.002   PHE A  78 
 TRP   0.007   0.001   TRP L 141 
 HIS   0.009   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.18 (14864)
  covalent geometry    : angle       0.61657 /  0.35 (21353)
  hydrogen bonds       : bond        0.06360 /  4.23 (  810)
  hydrogen bonds       : angle       3.31097 /  2.35 ( 2059)
  metal coordination   : bond        0.01330 /  0.60 (    8)
  metal coordination   : angle       2.99787 /  1.35 (    9)
  link_TRANS           : bond        0.00048 /  0.02 (    2)
  link_TRANS           : angle       0.40964 /  0.19 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7882 (t0) cc_final: 0.7386 (t0)
REVERT: L   99 ILE cc_start: 0.6451 (mm) cc_final: 0.6222 (mp)
  outliers start: 5
  outliers final: 5
  residues processed: 101
  average time/residue: 0.1644
  time to fit residues: 22.6593
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   11 SER
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 68 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 98 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0970
   chunk 106 optimal weight:    3.9990
   chunk 112 optimal weight:   20.0000
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.175883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118586 restraints weight = 19526.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.36
r_work: 0.2818 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.0676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.150
  Angle     :  0.604   6.250  21368  Z= 0.345
  Chirality :  0.045   0.285   2419
  Planarity :  0.004   0.043   1688
  Dihedral  : 29.872 173.744   4332
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  8.53 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.48 (0.27), residues: 983
  helix:  2.26 (0.21), residues: 624
  sheet:  0.28 (1.06), residues: 21
  loop : -1.54 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  92 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.005   0.001   TRP K  77 
 HIS   0.004   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.15 (14864)
  covalent geometry    : angle       0.60060 /  0.35 (21353)
  hydrogen bonds       : bond        0.06022 /  4.00 (  810)
  hydrogen bonds       : angle       3.27170 /  2.32 ( 2059)
  metal coordination   : bond        0.01063 /  0.47 (    8)
  metal coordination   : angle       2.96203 /  1.31 (    9)
  link_TRANS           : bond        0.00045 /  0.02 (    2)
  link_TRANS           : angle       0.46160 /  0.22 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7833 (t0) cc_final: 0.7376 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1493
  time to fit residues: 19.9085
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:   10.0000
   chunk 118 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0020
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.6388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.174794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121448 restraints weight = 27458.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.80
r_work: 0.2953 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.0716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  14874  Z= 0.138
  Angle     :  0.597   6.675  21368  Z= 0.342
  Chirality :  0.045   0.272   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.846 174.053   4332
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.23 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.58 (0.27), residues: 983
  helix:  2.34 (0.21), residues: 624
  sheet:  0.30 (1.05), residues: 21
  loop : -1.51 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  99 
 TYR   0.009   0.001   TYR D 121 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.005   0.001   TRP L  33 
 HIS   0.003   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.14 (14864)
  covalent geometry    : angle       0.59434 /  0.34 (21353)
  hydrogen bonds       : bond        0.05746 /  3.79 (  810)
  hydrogen bonds       : angle       3.21249 /  2.28 ( 2059)
  metal coordination   : bond        0.00899 /  0.40 (    8)
  metal coordination   : angle       2.85617 /  1.26 (    9)
  link_TRANS           : bond        0.00086 /  0.04 (    2)
  link_TRANS           : angle       0.38020 /  0.18 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7927 (t0) cc_final: 0.7478 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 97
  average time/residue: 0.1648
  time to fit residues: 21.6726
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 99 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 34 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.173998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115557 restraints weight = 19890.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.51
r_work: 0.2721 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.0800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14874  Z= 0.157
  Angle     :  0.592   6.391  21368  Z= 0.339
  Chirality :  0.044   0.286   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.866 174.260   4332
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.58 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.54 (0.27), residues: 983
  helix:  2.32 (0.21), residues: 624
  sheet:  0.30 (1.05), residues: 21
  loop : -1.54 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.006   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.16 (14864)
  covalent geometry    : angle       0.58888 /  0.34 (21353)
  hydrogen bonds       : bond        0.05821 /  3.85 (  810)
  hydrogen bonds       : angle       3.17187 /  2.25 ( 2059)
  metal coordination   : bond        0.00994 /  0.44 (    8)
  metal coordination   : angle       2.86418 /  1.28 (    9)
  link_TRANS           : bond        0.00054 /  0.03 (    2)
  link_TRANS           : angle       0.35012 /  0.17 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.8023 (t0) cc_final: 0.7683 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 101
  average time/residue: 0.1569
  time to fit residues: 21.5123
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   11 SER
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 96 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.174593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.117525 restraints weight = 19375.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.39
r_work: 0.2816 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.2581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.0811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  14874  Z= 0.153
  Angle     :  0.590   6.680  21368  Z= 0.338
  Chirality :  0.044   0.284   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.865 174.317   4332
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.16 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.55 (0.27), residues: 983
  helix:  2.32 (0.21), residues: 624
  sheet:  0.34 (1.04), residues: 21
  loop : -1.53 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.011   0.001   PHE A  78 
 TRP   0.005   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.15 (14864)
  covalent geometry    : angle       0.58744 /  0.34 (21353)
  hydrogen bonds       : bond        0.05765 /  3.81 (  810)
  hydrogen bonds       : angle       3.16246 /  2.24 ( 2059)
  metal coordination   : bond        0.00944 /  0.42 (    8)
  metal coordination   : angle       2.86673 /  1.27 (    9)
  link_TRANS           : bond        0.00029 /  0.01 (    2)
  link_TRANS           : angle       0.38998 /  0.19 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.8002 (t0) cc_final: 0.7670 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 96
  average time/residue: 0.1518
  time to fit residues: 19.8904
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 100 optimal weight:   20.0000
   chunk 95 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.172986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.119314 restraints weight = 24901.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.68
r_work: 0.2761 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14874  Z= 0.184
  Angle     :  0.616   6.564  21368  Z= 0.348
  Chirality :  0.046   0.298   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.992 173.061   4332
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.75 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.40 (0.27), residues: 983
  helix:  2.21 (0.21), residues: 624
  sheet:  0.38 (1.04), residues: 21
  loop : -1.61 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  92 
 TYR   0.012   0.002   TYR D 121 
 PHE   0.012   0.002   PHE A  78 
 TRP   0.007   0.001   TRP L 141 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 (14864)
  covalent geometry    : angle       0.61348 /  0.35 (21353)
  hydrogen bonds       : bond        0.06313 /  4.20 (  810)
  hydrogen bonds       : angle       3.20122 /  2.27 ( 2059)
  metal coordination   : bond        0.01215 /  0.55 (    8)
  metal coordination   : angle       2.96921 /  1.35 (    9)
  link_TRANS           : bond        0.00030 /  0.02 (    2)
  link_TRANS           : angle       0.44197 /  0.20 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.8019 (t0) cc_final: 0.7618 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 97
  average time/residue: 0.1581
  time to fit residues: 20.6548
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.0670
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0970
   chunk 66 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   overall best weight:    0.4716

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.174818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.120133 restraints weight = 27440.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.87
r_work: 0.2852 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.0901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  14874  Z= 0.132
  Angle     :  0.597   7.167  21368  Z= 0.339
  Chirality :  0.045   0.268   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.910 172.884   4332
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.63 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.68 (0.27), residues: 983
  helix:  2.44 (0.21), residues: 624
  sheet:  0.38 (1.05), residues: 21
  loop : -1.50 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG G  99 
 TYR   0.012   0.001   TYR L  74 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.13 (14864)
  covalent geometry    : angle       0.59410 /  0.34 (21353)
  hydrogen bonds       : bond        0.05523 /  3.65 (  810)
  hydrogen bonds       : angle       3.14593 /  2.23 ( 2059)
  metal coordination   : bond        0.00826 /  0.36 (    8)
  metal coordination   : angle       2.86555 /  1.30 (    9)
  link_TRANS           : bond        0.00155 /  0.08 (    2)
  link_TRANS           : angle       0.35441 /  0.16 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7962 (t0) cc_final: 0.7585 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 97
  average time/residue: 0.1650
  time to fit residues: 21.6043
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 119 optimal weight:    0.0170
   chunk 43 optimal weight:    0.9980
   chunk 114 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 97 optimal weight:   10.9990
   chunk 50 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 72 optimal weight:   20.0000
   overall best weight:    0.8820

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.173770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.123323 restraints weight = 25746.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.83
r_work: 0.2908 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.0924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  14874  Z= 0.141
  Angle     :  0.591   8.406  21368  Z= 0.336
  Chirality :  0.044   0.284   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.936 174.641   4332
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.75 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.66 (0.27), residues: 983
  helix:  2.42 (0.21), residues: 625
  sheet:  0.39 (1.05), residues: 21
  loop : -1.51 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  99 
 TYR   0.011   0.001   TYR L  74 
 PHE   0.009   0.001   PHE A  78 
 TRP   0.007   0.001   TRP L 141 
 HIS   0.003   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.14 (14864)
  covalent geometry    : angle       0.58833 /  0.34 (21353)
  hydrogen bonds       : bond        0.05640 /  3.71 (  810)
  hydrogen bonds       : angle       3.11307 /  2.21 ( 2059)
  metal coordination   : bond        0.01023 /  0.46 (    8)
  metal coordination   : angle       2.86539 /  1.30 (    9)
  link_TRANS           : bond        0.00039 /  0.02 (    2)
  link_TRANS           : angle       0.35763 /  0.16 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.8070 (t0) cc_final: 0.7688 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 97
  average time/residue: 0.1509
  time to fit residues: 19.8167
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 92 optimal weight:    9.9990
   chunk 115 optimal weight:    0.0770
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.175193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.116867 restraints weight = 19497.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.50
r_work: 0.2732 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2581 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  14874  Z= 0.133
  Angle     :  0.586   9.555  21368  Z= 0.334
  Chirality :  0.044   0.275   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.914 174.292   4332
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.86 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.68 (0.27), residues: 983
  helix:  2.42 (0.21), residues: 625
  sheet:  0.38 (1.05), residues: 21
  loop : -1.49 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  99 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.007   0.001   TRP L 141 
 HIS   0.003   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.13 (14864)
  covalent geometry    : angle       0.58313 /  0.33 (21353)
  hydrogen bonds       : bond        0.05558 /  3.66 (  810)
  hydrogen bonds       : angle       3.09999 /  2.20 ( 2059)
  metal coordination   : bond        0.00939 /  0.42 (    8)
  metal coordination   : angle       2.82232 /  1.27 (    9)
  link_TRANS           : bond        0.00045 /  0.02 (    2)
  link_TRANS           : angle       0.33411 /  0.15 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3299.29 seconds
wall clock time: 57 minutes 1.01 seconds (3421.01 seconds total)