Starting phenix.real_space_refine
on Fri Aug  7 00:45:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smy_40606/08_2026/8smy_40606.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.115
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 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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      32.961  68.212  47.437  1.00 46.50           S
  ATOM  12446  SG  CYS K  51      31.741  64.804  46.427  1.00 38.48           S
  ATOM  12470  SG  CYS K  54      31.689  67.804  43.930  1.00 45.98           S
  ATOM  12187  SG  CYS K  16      23.164  61.088  52.931  1.00 62.13           S
  ATOM  12205  SG  CYS K  19      21.277  58.686  55.106  1.00 60.25           S
  ATOM  12335  SG  CYS K  36      24.123  60.787  56.601  1.00 49.24           S
  ATOM  12357  SG  CYS K  39      25.001  57.974  54.445  1.00 47.55           S

  Time building chain proxies: 3.51, per 1000 atoms: 0.25
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 130.144, 127.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2608      7.00
     C    7891      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 494.9 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  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        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
      63.4% alpha, 4.3% beta
      137 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 1.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 55
      removed outlier: 3.697A  pdb=" N   ILE A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.706A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.642A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.836A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.608A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.724A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.737A  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: 3.541A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.564A  pdb=" N   MET D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 3.661A  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: 4.180A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.618A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU E 105 " --> pdb=" O   VAL E 101 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.881A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.595A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.757A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 90
    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: 3.620A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 4.044A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.656A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.887A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.703A  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 145
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.687A  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
      removed outlier: 3.535A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.696A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.458A  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 101 through 102
      removed outlier: 6.826A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.097A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.767A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 29
      removed outlier: 3.788A  pdb=" N   HIS K  33 " --> pdb=" O   LEU K  29 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25

    452 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      351 hydrogen bonds
      698 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 1.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3240
        1.34 -     1.46: 4293
        1.46 -     1.58: 6698
        1.58 -     1.70: 586
        1.70 -     1.82: 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  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.10e+01
  bond pdb=" C3'  DT I  62 "
       pdb=" C2'  DT I  62 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.02e+01
  bond pdb=" C3'  DT J -17 "
       pdb=" C2'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.23e+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 9.10e+00
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 20451
        1.75 -     3.50: 878
        3.50 -     5.25: 20
        5.25 -     6.99: 2
        6.99 -     8.74: 2
  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  103.19    2.81 6.00e-01 2.78e+00 2.20e+01
  angle pdb=" N3   DT I -43 "
        pdb=" C4   DT I -43 "
        pdb=" O4   DT I -43 "
      ideal   model   delta    sigma   weight residual
     119.90  122.56   -2.66 6.00e-01 2.78e+00 1.96e+01
  angle pdb=" N3   DT J -17 "
        pdb=" C4   DT J -17 "
        pdb=" O4   DT J -17 "
      ideal   model   delta    sigma   weight residual
     119.90  122.55   -2.65 6.00e-01 2.78e+00 1.95e+01
  angle pdb=" N3   DT I -42 "
        pdb=" C4   DT I -42 "
        pdb=" O4   DT I -42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.55   -2.65 6.00e-01 2.78e+00 1.95e+01
  angle pdb=" N3   DT J   9 "
        pdb=" C4   DT J   9 "
        pdb=" O4   DT J   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.91e+01
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.30: 6813
       35.30 -    70.59: 1393
       70.59 -   105.89: 22
      105.89 -   141.19: 0
      141.19 -   176.49: 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   43.51  176.49     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   66.28  153.72     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CB  GLU G  41 "
           pdb=" CG  GLU G  41 "
           pdb=" CD  GLU G  41 "
           pdb=" OE1 GLU G  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.70  -89.70     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1367
       0.031 -    0.063: 705
       0.063 -    0.094: 259
       0.094 -    0.125: 85
       0.125 -    0.157: 3
  Chirality restraints: 2419
  Sorted by residual:
  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 6.14e-01
  chirality pdb=" C3'  DC J  49 "
            pdb=" C4'  DC J  49 "
            pdb=" O3'  DC J  49 "
            pdb=" C2'  DC J  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.60   -0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  ILE G  79 "
            pdb=" N   ILE G  79 "
            pdb=" C   ILE G  79 "
            pdb=" CB  ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "   -0.053 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO L  61 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  42 "   -0.182 9.50e-02 1.11e+02   8.19e-02 4.21e+00
        pdb=" NE  ARG A  42 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  42 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  42 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  42 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS L  75 "   -0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO L  76 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO L  76 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO L  76 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 610
        2.71 -     3.26: 12002
        3.26 -     3.80: 24351
        3.80 -     4.35: 31976
        4.35 -     4.90: 46643
  Nonbonded interactions: 115582
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  73 "
            pdb=" ND2 ASN B  25 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" OG  SER K  60 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.244 2.496
  nonbonded pdb=" O   LEU E  61 "
            pdb=" NH1 ARG F  36 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.271 3.120
  ... (remaining 115577 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:             1.410
  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:             0.020
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.350
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
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   0.039  14874  Z= 0.476
  Angle     :  0.704   8.742  21368  Z= 0.612
  Chirality :  0.043   0.157   2419
  Planarity :  0.005   0.082   1688
  Dihedral  : 26.398 176.486   6336
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.27), residues: 983
  helix:  1.87 (0.22), residues: 613
  sheet:  0.67 (1.00), residues: 24
  loop : -0.77 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K  68 
 TYR   0.012   0.001   TYR L 134 
 PHE   0.009   0.001   PHE F  61 
 TRP   0.006   0.001   TRP K  77 
 HIS   0.005   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00525 /  0.48 (14864)
  covalent geometry    : angle       0.70070 /  0.61 (21353)
  hydrogen bonds       : bond        0.11106 /  7.24 (  803)
  hydrogen bonds       : angle       3.48440 /  2.48 ( 2033)
  metal coordination   : bond        0.01386 /  0.70 (    8)
  metal coordination   : angle       3.50716 /  1.84 (    9)
  link_TRANS           : bond        0.00192 /  0.10 (    2)
  link_TRANS           : angle       0.58269 /  0.25 (    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
  117 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   58 THR cc_start: 0.9392 (p) cc_final: 0.9020 (p)
REVERT: B   63 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7675 (mt-10)
REVERT: G   74 LYS cc_start: 0.8650 (mttp) cc_final: 0.8190 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1606
  time to fit residues: 25.6759
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0170
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.6418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
F  27 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.174110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.125534 restraints weight = 28724.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.80
r_work: 0.2880 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 10 (16 function evaluations)
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.0509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14874  Z= 0.137
  Angle     :  0.598   7.392  21368  Z= 0.348
  Chirality :  0.044   0.275   2419
  Planarity :  0.005   0.052   1688
  Dihedral  : 29.416 177.747   4332
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.19 %
    Favored  : 93.22 %
  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:  1.47 (0.27), residues: 983
  helix:  1.87 (0.21), residues: 631
  sheet:  0.61 (0.99), residues: 24
  loop : -0.78 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  42 
 TYR   0.008   0.001   TYR D  40 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.006   0.001   TRP K  77 
 HIS   0.005   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.14 (14864)
  covalent geometry    : angle       0.59063 /  0.35 (21353)
  hydrogen bonds       : bond        0.05540 /  3.54 (  803)
  hydrogen bonds       : angle       3.08976 /  2.19 ( 2033)
  metal coordination   : bond        0.01526 /  0.78 (    8)
  metal coordination   : angle       4.46383 /  2.32 (    9)
  link_TRANS           : bond        0.00029 /  0.01 (    2)
  link_TRANS           : angle       0.53409 /  0.22 (    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
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9409 (p) cc_final: 0.9104 (p)
REVERT: B   63 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8109 (mt-10)
REVERT: D   76 GLU cc_start: 0.9073 (tp30) cc_final: 0.8697 (tp30)
REVERT: E   59 GLU cc_start: 0.8544 (pt0) cc_final: 0.8298 (pt0)
REVERT: G   74 LYS cc_start: 0.8735 (mttp) cc_final: 0.8246 (mmtm)
  outliers start: 5
  outliers final: 5
  residues processed: 109
  average time/residue: 0.1626
  time to fit residues: 24.3423
Evaluate side-chains
  106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain K residue   49 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 117 optimal weight:    0.0970
   chunk 82 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 29 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.155805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.109737 restraints weight = 25025.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 1.64
r_work: 0.2772 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2810
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.0692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14874  Z= 0.132
  Angle     :  0.570   6.698  21368  Z= 0.332
  Chirality :  0.043   0.280   2419
  Planarity :  0.004   0.044   1688
  Dihedral  : 29.433 177.759   4332
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.36 %
    Favored  : 91.59 %
  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:  1.61 (0.27), residues: 983
  helix:  1.99 (0.21), residues: 633
  sheet:  0.68 (0.99), residues: 24
  loop : -0.75 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  42 
 TYR   0.009   0.001   TYR D  40 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.006   0.001   TRP K  77 
 HIS   0.007   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.13 (14864)
  covalent geometry    : angle       0.56425 /  0.33 (21353)
  hydrogen bonds       : bond        0.05136 /  3.27 (  803)
  hydrogen bonds       : angle       2.93568 /  2.09 ( 2033)
  metal coordination   : bond        0.01456 /  0.74 (    8)
  metal coordination   : angle       4.09603 /  2.17 (    9)
  link_TRANS           : bond        0.00093 /  0.05 (    2)
  link_TRANS           : angle       0.28369 /  0.14 (    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
  112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9394 (p) cc_final: 0.9088 (p)
REVERT: B   63 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8021 (mt-10)
REVERT: G   74 LYS cc_start: 0.8731 (mttp) cc_final: 0.8242 (mmtm)
  outliers start: 9
  outliers final: 7
  residues processed: 107
  average time/residue: 0.1623
  time to fit residues: 23.7660
Evaluate side-chains
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   35 GLU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 119 optimal weight:    7.9990
   chunk 106 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0670
   overall best weight:    1.1324

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.170003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119623 restraints weight = 19905.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.22
r_work: 0.2784 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.0782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14874  Z= 0.154
  Angle     :  0.593   8.493  21368  Z= 0.339
  Chirality :  0.044   0.301   2419
  Planarity :  0.004   0.049   1688
  Dihedral  : 29.557 177.600   4332
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 10.05 %
    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:  1.51 (0.27), residues: 983
  helix:  1.94 (0.21), residues: 633
  sheet:  0.73 (0.99), residues: 24
  loop : -0.88 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  55 
 TYR   0.010   0.001   TYR C  50 
 PHE   0.009   0.001   PHE K  53 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.007   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 (14864)
  covalent geometry    : angle       0.58736 /  0.34 (21353)
  hydrogen bonds       : bond        0.05520 /  3.58 (  803)
  hydrogen bonds       : angle       2.93658 /  2.10 ( 2033)
  metal coordination   : bond        0.01262 /  0.65 (    8)
  metal coordination   : angle       4.06897 /  2.14 (    9)
  link_TRANS           : bond        0.00055 /  0.03 (    2)
  link_TRANS           : angle       0.48096 /  0.22 (    6)

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

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: B   63 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8106 (mt-10)
REVERT: G   74 LYS cc_start: 0.8768 (mttp) cc_final: 0.8297 (mmtm)
  outliers start: 10
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1598
  time to fit residues: 23.2287
Evaluate side-chains
  107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 61 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 118 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 113 optimal weight:    7.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.170482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119733 restraints weight = 27816.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.68
r_work: 0.2704 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.0807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14874  Z= 0.142
  Angle     :  0.584   8.033  21368  Z= 0.335
  Chirality :  0.044   0.294   2419
  Planarity :  0.004   0.049   1688
  Dihedral  : 29.555 177.689   4332
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.63 %
    Favored  : 87.97 %
  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:  2.01 (0.21), residues: 631
  sheet:  0.81 (1.00), residues: 24
  loop : -0.85 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  68 
 TYR   0.008   0.001   TYR D  40 
 PHE   0.021   0.001   PHE L  56 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.14 (14864)
  covalent geometry    : angle       0.57861 /  0.33 (21353)
  hydrogen bonds       : bond        0.05318 /  3.43 (  803)
  hydrogen bonds       : angle       2.92734 /  2.09 ( 2033)
  metal coordination   : bond        0.01240 /  0.64 (    8)
  metal coordination   : angle       3.97242 /  2.09 (    9)
  link_TRANS           : bond        0.00004 /  0.00 (    2)
  link_TRANS           : angle       0.46150 /  0.21 (    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
  110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8317 (mt-10)
REVERT: B   63 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: G   74 LYS cc_start: 0.8608 (mttp) cc_final: 0.8083 (mmtm)
REVERT: H   86 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.8002 (mmt-90)
REVERT: L    6 ILE cc_start: 0.7210 (mm) cc_final: 0.6989 (mm)
  outliers start: 12
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1591
  time to fit residues: 22.4853
Evaluate side-chains
  108 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 99 optimal weight:   20.0000
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 72 optimal weight:   20.0000
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   chunk 80 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.153896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.106065 restraints weight = 20683.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.29
r_work: 0.2777 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2631 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2602 r_free = 0.2602    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2602 r_free = 0.2602    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2602
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14874  Z= 0.137
  Angle     :  0.580   6.901  21368  Z= 0.333
  Chirality :  0.044   0.293   2419
  Planarity :  0.005   0.084   1688
  Dihedral  : 29.555 177.732   4332
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.28 %
    Favored  : 88.20 %
  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:  1.61 (0.27), residues: 983
  helix:  2.02 (0.21), residues: 631
  sheet:  0.82 (1.00), residues: 24
  loop : -0.83 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 139 
 TYR   0.008   0.001   TYR D  40 
 PHE   0.008   0.001   PHE L  56 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.14 (14864)
  covalent geometry    : angle       0.57449 /  0.33 (21353)
  hydrogen bonds       : bond        0.05267 /  3.40 (  803)
  hydrogen bonds       : angle       2.91406 /  2.08 ( 2033)
  metal coordination   : bond        0.01146 /  0.59 (    8)
  metal coordination   : angle       3.93494 /  2.07 (    9)
  link_TRANS           : bond        0.00089 /  0.04 (    2)
  link_TRANS           : angle       0.43522 /  0.19 (    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
  116 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8475 (mt-10)
REVERT: B   63 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8147 (mt-10)
REVERT: G   74 LYS cc_start: 0.8686 (mttp) cc_final: 0.8190 (mmtm)
REVERT: H   86 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.8057 (mmt-90)
REVERT: L    6 ILE cc_start: 0.7355 (mm) cc_final: 0.7097 (mm)
  outliers start: 13
  outliers final: 12
  residues processed: 108
  average time/residue: 0.1595
  time to fit residues: 23.6539
Evaluate side-chains
  114 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0070
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0870
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.4576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.170218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119768 restraints weight = 20063.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.33
r_work: 0.3121 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.0826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056  14874  Z= 0.126
  Angle     :  0.577   7.318  21368  Z= 0.332
  Chirality :  0.043   0.288   2419
  Planarity :  0.005   0.109   1688
  Dihedral  : 29.543 177.526   4332
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.40 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.27), residues: 983
  helix:  2.08 (0.21), residues: 631
  sheet:  0.89 (1.01), residues: 24
  loop : -0.81 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  55 
 TYR   0.008   0.001   TYR D  40 
 PHE   0.015   0.001   PHE L  56 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00210 /  0.13 (14864)
  covalent geometry    : angle       0.57140 /  0.33 (21353)
  hydrogen bonds       : bond        0.05115 /  3.29 (  803)
  hydrogen bonds       : angle       2.90479 /  2.07 ( 2033)
  metal coordination   : bond        0.01153 /  0.59 (    8)
  metal coordination   : angle       3.87355 /  2.05 (    9)
  link_TRANS           : bond        0.00043 /  0.02 (    2)
  link_TRANS           : angle       0.40664 /  0.18 (    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
  112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8218 (mt-10)
REVERT: B   63 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7975 (mt-10)
REVERT: G   74 LYS cc_start: 0.8643 (mttp) cc_final: 0.8127 (mmtm)
REVERT: H   86 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.8019 (mmt-90)
REVERT: L    6 ILE cc_start: 0.7496 (mm) cc_final: 0.7204 (mm)
  outliers start: 12
  outliers final: 11
  residues processed: 104
  average time/residue: 0.1497
  time to fit residues: 21.1936
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0270
   chunk 95 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.4980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.170224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.121436 restraints weight = 25581.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.67
r_work: 0.3042 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2773 r_free = 0.2773    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2773 r_free = 0.2773    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.2773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  14874  Z= 0.131
  Angle     :  0.576   6.972  21368  Z= 0.331
  Chirality :  0.043   0.286   2419
  Planarity :  0.005   0.132   1688
  Dihedral  : 29.543 177.825   4332
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.98 %
    Favored  : 87.73 %
  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:  1.67 (0.27), residues: 983
  helix:  2.06 (0.21), residues: 632
  sheet:  0.86 (1.01), residues: 24
  loop : -0.80 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 139 
 TYR   0.008   0.001   TYR D  40 
 PHE   0.011   0.001   PHE L  56 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.13 (14864)
  covalent geometry    : angle       0.57037 /  0.33 (21353)
  hydrogen bonds       : bond        0.05124 /  3.30 (  803)
  hydrogen bonds       : angle       2.89354 /  2.07 ( 2033)
  metal coordination   : bond        0.01125 /  0.58 (    8)
  metal coordination   : angle       3.84393 /  2.03 (    9)
  link_TRANS           : bond        0.00082 /  0.04 (    2)
  link_TRANS           : angle       0.38643 /  0.17 (    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
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8275 (mt-10)
REVERT: B   63 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8034 (mt-10)
REVERT: G   74 LYS cc_start: 0.8656 (mttp) cc_final: 0.8136 (mmtm)
REVERT: H   86 ARG cc_start: 0.8305 (mmt-90) cc_final: 0.8043 (mmt-90)
REVERT: L    6 ILE cc_start: 0.7475 (mm) cc_final: 0.7173 (mm)
  outliers start: 11
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1561
  time to fit residues: 21.9515
Evaluate side-chains
  110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 113 optimal weight:    0.8980
   chunk 51 optimal weight:    0.3980
   chunk 116 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:    9.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.164582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.119704 restraints weight = 28518.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.88
r_work: 0.3048 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.2684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.0858

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= 0.134
  Angle     :  0.576   6.999  21368  Z= 0.331
  Chirality :  0.043   0.291   2419
  Planarity :  0.004   0.046   1688
  Dihedral  : 29.549 178.023   4332
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.63 %
    Favored  : 87.73 %
  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:  1.67 (0.27), residues: 983
  helix:  2.06 (0.21), residues: 632
  sheet:  0.82 (1.01), residues: 24
  loop : -0.80 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  55 
 TYR   0.008   0.001   TYR D  40 
 PHE   0.016   0.001   PHE L  56 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.005   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.13 (14864)
  covalent geometry    : angle       0.57104 /  0.33 (21353)
  hydrogen bonds       : bond        0.05108 /  3.28 (  803)
  hydrogen bonds       : angle       2.87608 /  2.05 ( 2033)
  metal coordination   : bond        0.01158 /  0.60 (    8)
  metal coordination   : angle       3.82346 /  2.03 (    9)
  link_TRANS           : bond        0.00093 /  0.05 (    2)
  link_TRANS           : angle       0.35580 /  0.16 (    6)

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

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: B   63 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8057 (mt-10)
REVERT: C   92 GLU cc_start: 0.8942 (mp0) cc_final: 0.8487 (mt-10)
REVERT: G   74 LYS cc_start: 0.8669 (mttp) cc_final: 0.8154 (mmtm)
REVERT: H   86 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.8047 (mmt-90)
REVERT: L    6 ILE cc_start: 0.7474 (mm) cc_final: 0.7195 (mm)
  outliers start: 14
  outliers final: 12
  residues processed: 104
  average time/residue: 0.1478
  time to fit residues: 20.8736
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue    1 MET
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  111 ASP
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:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 119 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 114 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 72 optimal weight:   20.0000
   overall best weight:    1.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  73 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.164810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.112222 restraints weight = 25716.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.59
r_work: 0.2794 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (13 function evaluations)
r_final: 0.2633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.0961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14874  Z= 0.197
  Angle     :  0.639   7.578  21368  Z= 0.356
  Chirality :  0.047   0.314   2419
  Planarity :  0.005   0.050   1688
  Dihedral  : 29.733 177.187   4332
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.98 %
    Favored  : 87.73 %
  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:  1.29 (0.27), residues: 983
  helix:  1.81 (0.21), residues: 631
  sheet:  0.69 (1.02), residues: 24
  loop : -1.04 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  55 
 TYR   0.013   0.002   TYR C  50 
 PHE   0.016   0.002   PHE L  56 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.007   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.20 (14864)
  covalent geometry    : angle       0.63351 /  0.36 (21353)
  hydrogen bonds       : bond        0.06201 /  4.07 (  803)
  hydrogen bonds       : angle       2.98858 /  2.14 ( 2033)
  metal coordination   : bond        0.01375 /  0.71 (    8)
  metal coordination   : angle       4.22694 /  2.21 (    9)
  link_TRANS           : bond        0.00020 /  0.01 (    2)
  link_TRANS           : angle       0.47548 /  0.20 (    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
  106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8337 (mt-10)
REVERT: G   74 LYS cc_start: 0.8868 (mttp) cc_final: 0.8356 (mmtm)
REVERT: H   86 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.8081 (mmt-90)
REVERT: L    6 ILE cc_start: 0.7427 (mm) cc_final: 0.7145 (mm)
REVERT: L  139 ARG cc_start: 0.7077 (mtt90) cc_final: 0.6488 (mmt-90)
  outliers start: 11
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1543
  time to fit residues: 21.5233
Evaluate side-chains
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue   38 MET
Chi-restraints excluded: chain L residue   54 ILE
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  111 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 109 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 98 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 92 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.166281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114390 restraints weight = 19741.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.38
r_work: 0.2738 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2600 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.0936

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= 0.139
  Angle     :  0.610   8.097  21368  Z= 0.343
  Chirality :  0.045   0.295   2419
  Planarity :  0.005   0.048   1688
  Dihedral  : 29.709 177.193   4332
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.10 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.27), residues: 983
  helix:  1.91 (0.21), residues: 630
  sheet:  0.70 (1.01), residues: 24
  loop : -1.03 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  55 
 TYR   0.008   0.001   TYR B  51 
 PHE   0.016   0.001   PHE L  56 
 TRP   0.007   0.001   TRP K  61 
 HIS   0.006   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.14 (14864)
  covalent geometry    : angle       0.60463 /  0.34 (21353)
  hydrogen bonds       : bond        0.05629 /  3.67 (  803)
  hydrogen bonds       : angle       2.95845 /  2.12 ( 2033)
  metal coordination   : bond        0.01355 /  0.69 (    8)
  metal coordination   : angle       4.07133 /  2.14 (    9)
  link_TRANS           : bond        0.00022 /  0.01 (    2)
  link_TRANS           : angle       0.45241 /  0.19 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3278.85 seconds
wall clock time: 56 minutes 37.05 seconds (3397.05 seconds total)