Starting phenix.real_space_refine
on Sat Jul  4 04:33:50 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn1_40609/07_2026/8sn1_40609.map"
  }
  resolution = 3.3
  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=   0.107
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
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 11 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      34.621  67.720  41.713  1.00 71.54           S
  ATOM  12446  SG  CYS K  51      32.912  64.309  42.021  1.00 58.73           S
  ATOM  12470  SG  CYS K  54      34.765  65.302  38.806  1.00 65.25           S
  ATOM  12187  SG  CYS K  16      21.868  63.309  48.158  1.00 77.69           S
  ATOM  12205  SG  CYS K  19      21.177  60.743  51.004  1.00 79.04           S
  ATOM  12335  SG  CYS K  36      23.454  63.950  51.370  1.00 71.93           S
  ATOM  12357  SG  CYS K  39      24.693  61.015  49.965  1.00 70.40           S

  Time building chain proxies: 3.15, per 1000 atoms: 0.23
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (110.224, 130.144, 124.832, 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: 1.22
  Conformation dependent library (CDL) restraints added in 488.4 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  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      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:
      43 helices and 11 sheets defined
      64.3% alpha, 4.4% beta
      135 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 1.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.564A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.585A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.924A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.877A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.591A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.659A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.693A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.558A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.782A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.535A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.822A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.624A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.678A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.782A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU E 126 " --> pdb=" O   LYS E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.744A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.898A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.573A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.522A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.642A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.613A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.764A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 3.674A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.766A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.772A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   HIS K  83 " --> pdb=" O   ILE K  79 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 86 through 91
      removed outlier: 4.374A  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 86 through 91
      removed outlier: 3.718A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
    Processing helix  chain 'L' and resid 131 through 143
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.200A  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: 7.435A  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 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.252A  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 77 through 78
      removed outlier: 3.550A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  53 " (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

    458 hydrogen bonds defined for protein.
    1356 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 1.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2909
        1.33 -     1.45: 4520
        1.45 -     1.57: 6802
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.28e+01
  bond pdb=" C3'  DT J -17 "
       pdb=" C2'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.07e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.34e+00
  bond pdb=" C3'  DC I  21 "
       pdb=" C2'  DC I  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.88e+00
  bond pdb=" C3'  DT I  62 "
       pdb=" C2'  DT I  62 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.82e+00
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 19350
        1.13 -     2.26: 1549
        2.26 -     3.39: 427
        3.39 -     4.51: 13
        4.51 -     5.64: 14
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" O4'  DT I -26 "
        pdb=" C4'  DT I -26 "
        pdb=" C3'  DT I -26 "
      ideal   model   delta    sigma   weight residual
     106.00  102.86    3.14 6.00e-01 2.78e+00 2.73e+01
  angle pdb=" O4'  DA J  42 "
        pdb=" C4'  DA J  42 "
        pdb=" C3'  DA J  42 "
      ideal   model   delta    sigma   weight residual
     106.00  102.96    3.04 6.00e-01 2.78e+00 2.57e+01
  angle pdb=" O4'  DA J  43 "
        pdb=" C4'  DA J  43 "
        pdb=" C3'  DA J  43 "
      ideal   model   delta    sigma   weight residual
     106.00  103.10    2.90 6.00e-01 2.78e+00 2.33e+01
  angle pdb=" N3   DT J  35 "
        pdb=" C4   DT J  35 "
        pdb=" O4   DT J  35 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.90e+01
  angle pdb=" N3   DT I  31 "
        pdb=" C4   DT I  31 "
        pdb=" O4   DT I  31 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.89e+01
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 6800
       35.27 -    70.54: 1406
       70.54 -   105.81: 22
      105.81 -   141.08: 0
      141.08 -   176.35: 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   43.65  176.35     1      3.50e+01 8.16e-04 1.57e+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   70.74  149.26     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CB  GLU G  91 "
           pdb=" CG  GLU G  91 "
           pdb=" CD  GLU G  91 "
           pdb=" OE1 GLU G  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.86  -89.86     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1452
       0.034 -    0.067: 661
       0.067 -    0.101: 241
       0.101 -    0.134: 61
       0.134 -    0.168: 4
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.04e-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   -2.57   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  VAL L  67 "
            pdb=" N   VAL L  67 "
            pdb=" C   VAL L  67 "
            pdb=" CB  VAL L  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.22e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO L  61 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.025 2.00e-02 2.50e+03   1.09e-02 3.24e+00
        pdb=" N9   DA I -35 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.004 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 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 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 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.028 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO D 103 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2255
        2.78 -     3.31: 12147
        3.31 -     3.84: 25337
        3.84 -     4.37: 30734
        4.37 -     4.90: 44982
  Nonbonded interactions: 115455
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.273 2.496
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" N3   DC I  21 "
            pdb=" N1   DG J -21 "
     model   vdw
     2.318 2.560
  ... (remaining 115450 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:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.540
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
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      :  0.005   0.045  14874  Z= 0.472
  Angle     :  0.698  12.165  21368  Z= 0.604
  Chirality :  0.043   0.168   2419
  Planarity :  0.004   0.047   1688
  Dihedral  : 26.479 176.350   6336
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.23 %
    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:  1.60 (0.27), residues: 983
  helix:  2.10 (0.21), residues: 628
  sheet: -0.62 (1.11), residues: 24
  loop : -0.89 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 129 
 TYR   0.020   0.001   TYR C  50 
 PHE   0.010   0.001   PHE L  69 
 TRP   0.017   0.002   TRP K  61 
 HIS   0.004   0.001   HIS C  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00522 /  0.47 (14864)
  covalent geometry    : angle       0.68395 /  0.60 (21353)
  hydrogen bonds       : bond        0.10626 /  6.85 (  805)
  hydrogen bonds       : angle       3.65213 /  2.68 ( 2046)
  metal coordination   : bond        0.00657 /  0.43 (    8)
  metal coordination   : angle       6.93178 /  3.40 (    9)
  link_TRANS           : bond        0.00103 /  0.05 (    2)
  link_TRANS           : angle       0.45456 /  0.20 (    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
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   99 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7258 (mtm180)
REVERT: E  122 LYS cc_start: 0.8891 (pttt) cc_final: 0.8580 (ptmt)
REVERT: E  129 ARG cc_start: 0.8628 (tmt170) cc_final: 0.8415 (tpt90)
REVERT: H   33 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7404 (mtt180)
REVERT: H   79 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8038 (mtm180)
REVERT: L  147 MET cc_start: 0.3445 (pmm) cc_final: 0.2318 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1660
  time to fit residues: 23.6348
Evaluate side-chains
  87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  41 GLN
L  46 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.157286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.112648 restraints weight = 29675.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 3.02
r_work: 0.2621 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2541 r_free = 0.2541    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2541 r_free = 0.2541    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.2541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.0640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.169
  Angle     :  0.616  11.163  21368  Z= 0.350
  Chirality :  0.045   0.282   2419
  Planarity :  0.005   0.043   1688
  Dihedral  : 29.831 176.979   4332
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  4.67 %
    Favored  : 94.63 %
  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:  1.59 (0.27), residues: 983
  helix:  2.12 (0.21), residues: 634
  sheet: -0.80 (1.08), residues: 24
  loop : -0.97 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  86 
 TYR   0.014   0.001   TYR C  50 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.012   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.17 (14864)
  covalent geometry    : angle       0.60281 /  0.35 (21353)
  hydrogen bonds       : bond        0.06200 /  4.11 (  805)
  hydrogen bonds       : angle       3.26392 /  2.44 ( 2046)
  metal coordination   : bond        0.00740 /  0.47 (    8)
  metal coordination   : angle       6.21505 /  3.07 (    9)
  link_TRANS           : bond        0.00036 /  0.02 (    2)
  link_TRANS           : angle       0.55560 /  0.26 (    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
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.370 
Fit side-chains
REVERT: C   36 LYS cc_start: 0.9138 (mttm) cc_final: 0.8765 (mtpp)
REVERT: D   47 GLN cc_start: 0.9052 (mt0) cc_final: 0.8838 (mt0)
REVERT: D   99 ARG cc_start: 0.8511 (mtt-85) cc_final: 0.7755 (mtm180)
REVERT: E  122 LYS cc_start: 0.9035 (pttt) cc_final: 0.8766 (ptmt)
REVERT: E  129 ARG cc_start: 0.8965 (tmt170) cc_final: 0.8558 (tpt90)
REVERT: G   73 ASN cc_start: 0.7894 (t0) cc_final: 0.7541 (t0)
REVERT: K   41 GLN cc_start: 0.6466 (mt0) cc_final: 0.6251 (mt0)
REVERT: L    4 LYS cc_start: 0.8030 (mttt) cc_final: 0.7791 (mttp)
REVERT: L  147 MET cc_start: 0.4047 (pmm) cc_final: 0.2852 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 93
  average time/residue: 0.1626
  time to fit residues: 20.4873
Evaluate side-chains
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 117 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:   20.0000
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.153929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.105645 restraints weight = 25434.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.30
r_work: 0.2619 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.0845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14874  Z= 0.189
  Angle     :  0.623  11.532  21368  Z= 0.349
  Chirality :  0.045   0.290   2419
  Planarity :  0.005   0.046   1688
  Dihedral  : 30.103 176.490   4332
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  7.48 %
    Favored  : 91.82 %
  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:  1.44 (0.27), residues: 983
  helix:  2.02 (0.21), residues: 633
  sheet: -0.78 (1.08), residues: 24
  loop : -1.09 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  35 
 TYR   0.011   0.001   TYR H 121 
 PHE   0.011   0.002   PHE F  61 
 TRP   0.012   0.001   TRP K  61 
 HIS   0.005   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.19 (14864)
  covalent geometry    : angle       0.61106 /  0.35 (21353)
  hydrogen bonds       : bond        0.06447 /  4.33 (  805)
  hydrogen bonds       : angle       3.24009 /  2.41 ( 2046)
  metal coordination   : bond        0.00794 /  0.51 (    8)
  metal coordination   : angle       5.99270 /  3.00 (    9)
  link_TRANS           : bond        0.00067 /  0.03 (    2)
  link_TRANS           : angle       0.53045 /  0.22 (    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
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9069 (mttm) cc_final: 0.8671 (mtpp)
REVERT: D   47 GLN cc_start: 0.8901 (mt0) cc_final: 0.8674 (mt0)
REVERT: D   99 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.7673 (mtm180)
REVERT: E  129 ARG cc_start: 0.8887 (tmt170) cc_final: 0.8494 (tpt90)
REVERT: G   73 ASN cc_start: 0.7998 (t0) cc_final: 0.7603 (t0)
REVERT: H   59 MET cc_start: 0.8941 (tpp) cc_final: 0.8453 (mmm)
REVERT: L  147 MET cc_start: 0.4142 (pmm) cc_final: 0.2871 (mtt)
  outliers start: 5
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1604
  time to fit residues: 19.8610
Evaluate side-chains
  89 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 27 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 119 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.153053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.105847 restraints weight = 25035.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.36
r_work: 0.2611 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2533 r_free = 0.2533    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2533 r_free = 0.2533    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  14874  Z= 0.210
  Angle     :  0.647  10.619  21368  Z= 0.357
  Chirality :  0.047   0.300   2419
  Planarity :  0.005   0.046   1688
  Dihedral  : 30.278 176.134   4332
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.00 %
    Favored  : 89.95 %
  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:  1.18 (0.27), residues: 983
  helix:  1.82 (0.21), residues: 639
  sheet: -0.74 (1.10), residues: 24
  loop : -1.27 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  35 
 TYR   0.013   0.001   TYR H 121 
 PHE   0.012   0.002   PHE F  61 
 TRP   0.011   0.001   TRP K  61 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00470 /  0.21 (14864)
  covalent geometry    : angle       0.63675 /  0.36 (21353)
  hydrogen bonds       : bond        0.06838 /  4.61 (  805)
  hydrogen bonds       : angle       3.25279 /  2.42 ( 2046)
  metal coordination   : bond        0.00885 /  0.54 (    8)
  metal coordination   : angle       5.67711 /  2.85 (    9)
  link_TRANS           : bond        0.00052 /  0.02 (    2)
  link_TRANS           : angle       0.59362 /  0.25 (    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
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.329 
Fit side-chains
REVERT: C   36 LYS cc_start: 0.9092 (mttm) cc_final: 0.8716 (mtpp)
REVERT: D   47 GLN cc_start: 0.8950 (mt0) cc_final: 0.8736 (mt0)
REVERT: D   99 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.7650 (mtm180)
REVERT: E  129 ARG cc_start: 0.8929 (tmt170) cc_final: 0.8547 (tpt90)
REVERT: G   73 ASN cc_start: 0.8085 (t0) cc_final: 0.7682 (t0)
REVERT: H   59 MET cc_start: 0.9035 (tpp) cc_final: 0.8455 (mmm)
REVERT: L  147 MET cc_start: 0.4202 (pmm) cc_final: 0.2996 (mtt)
  outliers start: 8
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1524
  time to fit residues: 19.0789
Evaluate side-chains
  91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   59 SER
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:   10.0000
   chunk 118 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.155196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.110275 restraints weight = 30073.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 2.97
r_work: 0.2606 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2527 r_free = 0.2527    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2527 r_free = 0.2527    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14874  Z= 0.147
  Angle     :  0.601   9.315  21368  Z= 0.336
  Chirality :  0.044   0.270   2419
  Planarity :  0.004   0.045   1688
  Dihedral  : 30.157 176.286   4332
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.28 %
    Favored  : 88.79 %
  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:  1.45 (0.27), residues: 983
  helix:  2.03 (0.21), residues: 639
  sheet: -0.81 (1.09), residues: 24
  loop : -1.13 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  35 
 TYR   0.008   0.001   TYR H 121 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.011   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 (14864)
  covalent geometry    : angle       0.59225 /  0.34 (21353)
  hydrogen bonds       : bond        0.05797 /  3.88 (  805)
  hydrogen bonds       : angle       3.11726 /  2.31 ( 2046)
  metal coordination   : bond        0.00638 /  0.38 (    8)
  metal coordination   : angle       4.94506 /  2.47 (    9)
  link_TRANS           : bond        0.00070 /  0.03 (    2)
  link_TRANS           : angle       0.50701 /  0.20 (    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
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.369 
Fit side-chains
REVERT: C   36 LYS cc_start: 0.9104 (mttm) cc_final: 0.8727 (mtpp)
REVERT: D   47 GLN cc_start: 0.8948 (mt0) cc_final: 0.8711 (mt0)
REVERT: D   99 ARG cc_start: 0.8493 (mtt-85) cc_final: 0.7673 (mtm180)
REVERT: E  129 ARG cc_start: 0.8951 (tmt170) cc_final: 0.8631 (tpt90)
REVERT: G   73 ASN cc_start: 0.8060 (t0) cc_final: 0.7632 (t0)
REVERT: H   59 MET cc_start: 0.9009 (tpp) cc_final: 0.8446 (mmm)
REVERT: L   92 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7939 (mm-40)
REVERT: L  147 MET cc_start: 0.4147 (pmm) cc_final: 0.2949 (mtt)
  outliers start: 7
  outliers final: 4
  residues processed: 96
  average time/residue: 0.1601
  time to fit residues: 21.0563
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 55 optimal weight:    0.4980
   chunk 51 optimal weight:    0.4980
   chunk 72 optimal weight:   20.0000
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.155506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.106727 restraints weight = 21917.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.93
r_work: 0.2653 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.0986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14874  Z= 0.145
  Angle     :  0.581   8.840  21368  Z= 0.329
  Chirality :  0.043   0.280   2419
  Planarity :  0.004   0.044   1688
  Dihedral  : 30.111 176.236   4332
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.33 %
    Favored  : 87.62 %
  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:  1.57 (0.27), residues: 983
  helix:  2.13 (0.21), residues: 639
  sheet: -0.73 (1.14), residues: 24
  loop : -1.13 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  35 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.010   0.001   TRP K  61 
 HIS   0.004   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.15 (14864)
  covalent geometry    : angle       0.57221 /  0.33 (21353)
  hydrogen bonds       : bond        0.05597 /  3.75 (  805)
  hydrogen bonds       : angle       3.07733 /  2.28 ( 2046)
  metal coordination   : bond        0.00585 /  0.37 (    8)
  metal coordination   : angle       4.81955 /  2.41 (    9)
  link_TRANS           : bond        0.00031 /  0.02 (    2)
  link_TRANS           : angle       0.38026 /  0.16 (    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
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9066 (mttm) cc_final: 0.8667 (mtpp)
REVERT: D   47 GLN cc_start: 0.8932 (mt0) cc_final: 0.8700 (mt0)
REVERT: D   99 ARG cc_start: 0.8420 (mtt-85) cc_final: 0.7639 (mtm180)
REVERT: E  129 ARG cc_start: 0.8897 (tmt170) cc_final: 0.8588 (tpt90)
REVERT: G   73 ASN cc_start: 0.7981 (t0) cc_final: 0.7520 (t0)
REVERT: H   59 MET cc_start: 0.8897 (tpp) cc_final: 0.8335 (mmm)
REVERT: L   52 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4196 (pp)
REVERT: L   92 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8007 (mm-40)
REVERT: L  147 MET cc_start: 0.4076 (pmm) cc_final: 0.2779 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1575
  time to fit residues: 21.7214
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  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
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:   10.9990
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.157005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.108275 restraints weight = 21124.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.80
r_work: 0.2733 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14874  Z= 0.138
  Angle     :  0.574   8.660  21368  Z= 0.326
  Chirality :  0.043   0.275   2419
  Planarity :  0.004   0.043   1688
  Dihedral  : 30.046 176.533   4332
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 12.73 %
    Favored  : 86.57 %
  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:  1.70 (0.27), residues: 983
  helix:  2.24 (0.21), residues: 639
  sheet: -0.76 (1.13), residues: 24
  loop : -1.09 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  35 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.008   0.001   PHE L  62 
 TRP   0.010   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.14 (14864)
  covalent geometry    : angle       0.56665 /  0.33 (21353)
  hydrogen bonds       : bond        0.05317 /  3.55 (  805)
  hydrogen bonds       : angle       3.03533 /  2.25 ( 2046)
  metal coordination   : bond        0.00520 /  0.32 (    8)
  metal coordination   : angle       4.63388 /  2.31 (    9)
  link_TRANS           : bond        0.00052 /  0.03 (    2)
  link_TRANS           : angle       0.48269 /  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
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9116 (mttm) cc_final: 0.8677 (mtpp)
REVERT: D   47 GLN cc_start: 0.8909 (mt0) cc_final: 0.8684 (mt0)
REVERT: D   99 ARG cc_start: 0.8415 (mtt-85) cc_final: 0.7637 (mtm180)
REVERT: E  129 ARG cc_start: 0.8873 (tmt170) cc_final: 0.8565 (tpt90)
REVERT: G   73 ASN cc_start: 0.7953 (t0) cc_final: 0.7501 (t0)
REVERT: H   59 MET cc_start: 0.8892 (tpp) cc_final: 0.8343 (mmm)
REVERT: L   92 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8031 (mm-40)
REVERT: L  147 MET cc_start: 0.3991 (pmm) cc_final: 0.2812 (mtt)
  outliers start: 5
  outliers final: 4
  residues processed: 97
  average time/residue: 0.1672
  time to fit residues: 22.0795
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0870
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0010
   chunk 95 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0030
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.3576

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.157548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.110079 restraints weight = 26227.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.37
r_work: 0.2651 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  14874  Z= 0.121
  Angle     :  0.560   8.339  21368  Z= 0.322
  Chirality :  0.042   0.261   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.999 176.248   4332
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.27 %
    Favored  : 86.68 %
  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:  1.83 (0.27), residues: 983
  helix:  2.34 (0.21), residues: 639
  sheet: -0.65 (1.13), residues: 24
  loop : -1.03 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  35 
 TYR   0.006   0.001   TYR F  51 
 PHE   0.011   0.001   PHE L  56 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00197 /  0.12 (14864)
  covalent geometry    : angle       0.55286 /  0.32 (21353)
  hydrogen bonds       : bond        0.05025 /  3.35 (  805)
  hydrogen bonds       : angle       3.00257 /  2.23 ( 2046)
  metal coordination   : bond        0.00461 /  0.29 (    8)
  metal coordination   : angle       4.46381 /  2.22 (    9)
  link_TRANS           : bond        0.00197 /  0.10 (    2)
  link_TRANS           : angle       0.44772 /  0.19 (    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
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9100 (mttm) cc_final: 0.8669 (mtpp)
REVERT: D   47 GLN cc_start: 0.8926 (mt0) cc_final: 0.8700 (mt0)
REVERT: D   99 ARG cc_start: 0.8424 (mtt-85) cc_final: 0.7620 (mtm180)
REVERT: E  122 LYS cc_start: 0.9037 (pttt) cc_final: 0.8726 (ptmt)
REVERT: E  129 ARG cc_start: 0.8862 (tmt170) cc_final: 0.8545 (tpt90)
REVERT: E  133 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8094 (pt0)
REVERT: G   73 ASN cc_start: 0.7946 (t0) cc_final: 0.7479 (t0)
REVERT: H   59 MET cc_start: 0.8871 (tpp) cc_final: 0.8356 (mmm)
REVERT: L   52 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4288 (pp)
REVERT: L   92 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7998 (mm-40)
REVERT: L  147 MET cc_start: 0.3851 (pmm) cc_final: 0.2746 (mtt)
  outliers start: 8
  outliers final: 6
  residues processed: 103
  average time/residue: 0.1648
  time to fit residues: 23.1642
Evaluate side-chains
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 92 optimal weight:   10.0000
   chunk 113 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 116 optimal weight:   10.0000
   chunk 66 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.160481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.113809 restraints weight = 29278.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.98
r_work: 0.2636 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2600 r_free = 0.2600    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14874  Z= 0.124
  Angle     :  0.543   8.106  21368  Z= 0.316
  Chirality :  0.041   0.268   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.879 177.183   4332
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.50 %
    Favored  : 86.45 %
  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:  1.99 (0.27), residues: 983
  helix:  2.44 (0.21), residues: 641
  sheet: -0.43 (1.16), residues: 24
  loop : -0.97 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  35 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.010   0.001   PHE L  56 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.12 (14864)
  covalent geometry    : angle       0.53627 /  0.32 (21353)
  hydrogen bonds       : bond        0.04777 /  3.19 (  805)
  hydrogen bonds       : angle       2.91610 /  2.16 ( 2046)
  metal coordination   : bond        0.00480 /  0.29 (    8)
  metal coordination   : angle       4.25870 /  2.14 (    9)
  link_TRANS           : bond        0.00068 /  0.03 (    2)
  link_TRANS           : angle       0.45914 /  0.20 (    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
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.346 
Fit side-chains
REVERT: C   36 LYS cc_start: 0.9087 (mttm) cc_final: 0.8705 (mtpp)
REVERT: D   47 GLN cc_start: 0.8982 (mt0) cc_final: 0.8741 (mt0)
REVERT: D   99 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.7711 (mtm180)
REVERT: E  122 LYS cc_start: 0.9016 (pttt) cc_final: 0.8690 (pttt)
REVERT: E  129 ARG cc_start: 0.8941 (tmt170) cc_final: 0.8600 (tpt90)
REVERT: E  133 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8014 (pt0)
REVERT: G   73 ASN cc_start: 0.7893 (t0) cc_final: 0.7460 (t0)
REVERT: H   59 MET cc_start: 0.8864 (tpp) cc_final: 0.8371 (mmm)
REVERT: L   52 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.4670 (pp)
REVERT: L  147 MET cc_start: 0.3995 (pmm) cc_final: 0.2800 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 101
  average time/residue: 0.1466
  time to fit residues: 20.4224
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  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
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:   10.0000
   chunk 119 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 72 optimal weight:   30.0000
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.3597 r_free = 0.3597 target = 0.154359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.107823 restraints weight = 26841.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.67
r_work: 0.2582 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14874  Z= 0.185
  Angle     :  0.618   8.739  21368  Z= 0.344
  Chirality :  0.045   0.298   2419
  Planarity :  0.005   0.043   1688
  Dihedral  : 30.135 176.490   4332
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.32 %
    Favored  : 85.75 %
  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:  2.13 (0.21), residues: 639
  sheet: -0.40 (1.18), residues: 24
  loop : -1.22 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  35 
 TYR   0.009   0.001   TYR H 121 
 PHE   0.011   0.002   PHE F  61 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.005   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.19 (14864)
  covalent geometry    : angle       0.61036 /  0.34 (21353)
  hydrogen bonds       : bond        0.06217 /  4.18 (  805)
  hydrogen bonds       : angle       3.11286 /  2.30 ( 2046)
  metal coordination   : bond        0.00596 /  0.38 (    8)
  metal coordination   : angle       4.64528 /  2.33 (    9)
  link_TRANS           : bond        0.00057 /  0.03 (    2)
  link_TRANS           : angle       0.61019 /  0.24 (    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
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9166 (mttm) cc_final: 0.8751 (mtpp)
REVERT: D   47 GLN cc_start: 0.8968 (mt0) cc_final: 0.8733 (mt0)
REVERT: D   99 ARG cc_start: 0.8477 (mtt-85) cc_final: 0.7654 (mtm180)
REVERT: E  129 ARG cc_start: 0.8836 (tmt170) cc_final: 0.8410 (tpt90)
REVERT: E  133 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8040 (pt0)
REVERT: G   73 ASN cc_start: 0.8014 (t0) cc_final: 0.7550 (t0)
REVERT: H   59 MET cc_start: 0.8983 (tpp) cc_final: 0.8356 (mmm)
REVERT: L   38 MET cc_start: 0.5064 (mtm) cc_final: 0.4810 (mmm)
REVERT: L   52 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4232 (pp)
REVERT: L   92 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8026 (mm-40)
REVERT: L  147 MET cc_start: 0.3815 (pmm) cc_final: 0.2674 (mtt)
  outliers start: 7
  outliers final: 5
  residues processed: 92
  average time/residue: 0.1515
  time to fit residues: 19.0800
Evaluate side-chains
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 109 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 98 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 92 optimal weight:   10.0000
   chunk 115 optimal weight:    8.9990
   chunk 52 optimal weight:    0.6980
   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 = 0.3616 r_free = 0.3616 target = 0.155768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.109763 restraints weight = 20657.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.68
r_work: 0.2677 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1135

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= 0.149
  Angle     :  0.593   8.558  21368  Z= 0.333
  Chirality :  0.043   0.279   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 30.100 176.915   4332
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.08 %
    Favored  : 85.86 %
  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:  2.16 (0.21), residues: 639
  sheet: -0.38 (1.18), residues: 24
  loop : -1.19 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  35 
 TYR   0.008   0.001   TYR B  51 
 PHE   0.014   0.002   PHE L  56 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.004   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.15 (14864)
  covalent geometry    : angle       0.58508 /  0.33 (21353)
  hydrogen bonds       : bond        0.05741 /  3.85 (  805)
  hydrogen bonds       : angle       3.06801 /  2.27 ( 2046)
  metal coordination   : bond        0.01045 /  0.56 (    8)
  metal coordination   : angle       4.61946 /  2.32 (    9)
  link_TRANS           : bond        0.00020 /  0.01 (    2)
  link_TRANS           : angle       0.51323 /  0.21 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3177.06 seconds
wall clock time: 55 minutes 0.15 seconds (3300.15 seconds total)