Starting phenix.real_space_refine
on Sat Jul  4 04:23:36 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8smx_40605/07_2026/8smx_40605.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.123
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7891      2.51       5
     N    2608      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13998
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      32.756  69.086  46.490  1.00 27.36           S
  ATOM  12446  SG  CYS K  51      31.674  65.517  46.031  1.00 24.79           S
  ATOM  12470  SG  CYS K  54      32.868  67.529  43.025  1.00 27.29           S
  ATOM  12187  SG  CYS K  16      23.703  62.014  53.077  1.00 58.61           S
  ATOM  12205  SG  CYS K  19      21.687  59.882  55.391  1.00 62.50           S
  ATOM  12335  SG  CYS K  36      23.658  62.811  56.830  1.00 42.90           S
  ATOM  12357  SG  CYS K  39      25.492  59.705  55.463  1.00 39.01           S

  Time building chain proxies: 3.35, per 1000 atoms: 0.24
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 130.144, 126.16, 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: 1.10
  Conformation dependent library (CDL) restraints added in 464.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
      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 12 sheets defined
      64.1% alpha, 4.5% beta
      136 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 2.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.611A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.565A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.844A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.593A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.740A  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: 3.508A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.640A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.764A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.538A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 123
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.761A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.579A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.588A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (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 41
      removed outlier: 3.585A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.819A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.684A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.559A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.641A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.574A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 37 through 46
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 3.858A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 74 through 84
      removed outlier: 4.158A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR K  84 " --> pdb=" O   ILE K  80 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.917A  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: 3.538A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.860A  pdb=" N   LEU L 110 " --> pdb=" O   ILE L 106 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ASP L 111 " --> pdb=" O   ALA L 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
    Processing helix  chain 'L' and resid 130 through 143
      removed outlier: 3.639A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.155A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.444A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.800A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.010A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.606A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25

    462 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 2.32

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2974
        1.33 -     1.45: 4495
        1.45 -     1.57: 6762
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DT J -72 "
       pdb=" C2'  DT J -72 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+01
  bond pdb=" C3'  DC I  21 "
       pdb=" C2'  DC I  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.83e+00
  bond pdb=" C3'  DA J -30 "
       pdb=" C2'  DA J -30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.46e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" C2'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.45e+00
  bond pdb=" C3'  DT I  62 "
       pdb=" C2'  DT I  62 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.23e+00
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 20417
        1.77 -     3.54: 904
        3.54 -     5.31: 25
        5.31 -     7.08: 5
        7.08 -     8.85: 2
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" N3   DT J -17 "
        pdb=" C4   DT J -17 "
        pdb=" O4   DT J -17 "
      ideal   model   delta    sigma   weight residual
     119.90  122.64   -2.74 6.00e-01 2.78e+00 2.08e+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  122.60   -2.70 6.00e-01 2.78e+00 2.03e+01
  angle pdb=" N3   DT I  38 "
        pdb=" C4   DT I  38 "
        pdb=" O4   DT I  38 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.02e+01
  angle pdb=" N3   DT I -59 "
        pdb=" C4   DT I -59 "
        pdb=" O4   DT I -59 "
      ideal   model   delta    sigma   weight residual
     119.90  122.59   -2.69 6.00e-01 2.78e+00 2.01e+01
  angle pdb=" O4'  DC J -25 "
        pdb=" C1'  DC J -25 "
        pdb=" N1   DC J -25 "
      ideal   model   delta    sigma   weight residual
     108.00  111.10   -3.10 7.00e-01 2.04e+00 1.97e+01
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.13: 6796
       35.13 -    70.26: 1411
       70.26 -   105.39: 21
      105.39 -   140.51: 0
      140.51 -   175.64: 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   44.36  175.64     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   66.14  153.86     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CA  PHE E  84 "
           pdb=" C   PHE E  84 "
           pdb=" N   GLN E  85 "
           pdb=" CA  GLN E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.10   16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1348
       0.031 -    0.062: 685
       0.062 -    0.093: 281
       0.093 -    0.124: 93
       0.124 -    0.155: 12
  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   -2.58   -0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CG  LEU L 103 "
            pdb=" CB  LEU L 103 "
            pdb=" CD1 LEU L 103 "
            pdb=" CD2 LEU L 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.56e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.026 2.00e-02 2.50e+03   1.14e-02 3.60e+00
        pdb=" N9   DA I -35 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.024 2.00e-02 2.50e+03   1.03e-02 3.20e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  17 "    0.024 2.00e-02 2.50e+03   1.06e-02 3.07e+00
        pdb=" N9   DA I  17 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8   DA I  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  17 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  17 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  17 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  17 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2062
        2.77 -     3.30: 11830
        3.30 -     3.83: 25259
        3.83 -     4.37: 31139
        4.37 -     4.90: 45796
  Nonbonded interactions: 116086
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.236 2.496
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" NZ  LYS D 116 "
            pdb=" O   ALA K  47 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" N3   DC I  21 "
            pdb=" N1   DG J -21 "
     model   vdw
     2.294 2.560
  ... (remaining 116081 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:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     16.280
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
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   0.040  14874  Z= 0.483
  Angle     :  0.718   8.854  21368  Z= 0.620
  Chirality :  0.044   0.155   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 26.376 175.642   6336
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.45
  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:  1.43 (0.27), residues: 983
  helix:  1.97 (0.21), residues: 628
  sheet: -0.51 (0.92), residues: 24
  loop : -0.96 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  45 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.006   0.001   TRP K  77 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00533 /  0.48 (14864)
  covalent geometry    : angle       0.71760 /  0.62 (21353)
  hydrogen bonds       : bond        0.11293 /  7.68 (  811)
  hydrogen bonds       : angle       3.76124 /  2.80 ( 2062)
  metal coordination   : bond        0.00466 /  0.22 (    8)
  metal coordination   : angle       1.84038 /  0.96 (    9)
  link_TRANS           : bond        0.00193 /  0.10 (    2)
  link_TRANS           : angle       0.44603 /  0.19 (    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
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.400 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7865 (pttm) cc_final: 0.7286 (ptpp)
REVERT: D   35 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: D  116 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7592 (mtmm)
REVERT: E   53 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8015 (ttm170)
REVERT: H   54 ILE cc_start: 0.9102 (tt) cc_final: 0.8879 (tt)
REVERT: H  112 SER cc_start: 0.9103 (t) cc_final: 0.8481 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1653
  time to fit residues: 22.1253
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    0.1980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.172227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.127105 restraints weight = 27183.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.74
r_work: 0.2819 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2638
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2638 r_free = 0.2638    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2638 r_free = 0.2638    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2638
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.0567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  14874  Z= 0.141
  Angle     :  0.601   6.452  21368  Z= 0.351
  Chirality :  0.044   0.249   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.537 178.037   4332
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.97 %
    Favored  : 95.91 %
  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:  1.71 (0.27), residues: 983
  helix:  2.21 (0.21), residues: 633
  sheet: -0.91 (0.87), residues: 24
  loop : -0.89 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  99 
 TYR   0.011   0.001   TYR G  50 
 PHE   0.008   0.001   PHE F  61 
 TRP   0.005   0.001   TRP K  77 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.14 (14864)
  covalent geometry    : angle       0.59869 /  0.35 (21353)
  hydrogen bonds       : bond        0.05786 /  4.07 (  811)
  hydrogen bonds       : angle       3.03683 /  2.24 ( 2062)
  metal coordination   : bond        0.00486 /  0.23 (    8)
  metal coordination   : angle       2.42351 /  1.25 (    9)
  link_TRANS           : bond        0.00056 /  0.03 (    2)
  link_TRANS           : angle       0.41540 /  0.18 (    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
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.365 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8098 (mt-10)
REVERT: C  118 LYS cc_start: 0.7758 (pttm) cc_final: 0.7073 (ptpp)
REVERT: D   35 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7837 (mt-10)
REVERT: H   54 ILE cc_start: 0.9279 (tt) cc_final: 0.9030 (tt)
REVERT: H  112 SER cc_start: 0.9176 (t) cc_final: 0.8532 (m)
REVERT: K   60 SER cc_start: 0.8604 (t) cc_final: 0.8307 (m)
REVERT: L   78 ILE cc_start: 0.5858 (mp) cc_final: 0.5513 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1468
  time to fit residues: 20.2424
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 117 optimal weight:    0.6980
   chunk 82 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   chunk 110 optimal weight:   40.0000
   overall best weight:    1.3186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.164281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.118897 restraints weight = 23493.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.59
r_work: 0.2674 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2603
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2603 r_free = 0.2603    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2603 r_free = 0.2603    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2603
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.0661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14874  Z= 0.173
  Angle     :  0.610   7.134  21368  Z= 0.351
  Chirality :  0.045   0.282   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.679 177.660   4332
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  5.61 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.27), residues: 983
  helix:  2.12 (0.21), residues: 634
  sheet: -0.70 (0.90), residues: 24
  loop : -1.00 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  45 
 TYR   0.016   0.001   TYR G  50 
 PHE   0.011   0.002   PHE D  65 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.005   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.17 (14864)
  covalent geometry    : angle       0.60868 /  0.35 (21353)
  hydrogen bonds       : bond        0.06158 /  4.27 (  811)
  hydrogen bonds       : angle       3.05167 /  2.24 ( 2062)
  metal coordination   : bond        0.00494 /  0.24 (    8)
  metal coordination   : angle       1.90922 /  1.06 (    9)
  link_TRANS           : bond        0.00076 /  0.04 (    2)
  link_TRANS           : angle       0.44085 /  0.21 (    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
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.375 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7951 (mt-10)
REVERT: C  118 LYS cc_start: 0.7847 (pttm) cc_final: 0.7088 (ptpp)
REVERT: D   35 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7887 (mt-10)
REVERT: H  112 SER cc_start: 0.9168 (t) cc_final: 0.8523 (m)
REVERT: K   60 SER cc_start: 0.8602 (t) cc_final: 0.8335 (m)
REVERT: L   78 ILE cc_start: 0.5993 (mp) cc_final: 0.5543 (tp)
  outliers start: 6
  outliers final: 4
  residues processed: 94
  average time/residue: 0.1742
  time to fit residues: 21.8861
Evaluate side-chains
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain L residue   88 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 83 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 119 optimal weight:   40.0000
   chunk 106 optimal weight:    0.0170
   chunk 112 optimal weight:   10.0000
   overall best weight:    1.7224

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.159473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.114583 restraints weight = 19696.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.30
r_work: 0.2720 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.0777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14874  Z= 0.200
  Angle     :  0.641   7.413  21368  Z= 0.361
  Chirality :  0.047   0.303   2419
  Planarity :  0.005   0.039   1688
  Dihedral  : 29.865 179.426   4332
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.54 %
    Favored  : 92.87 %
  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:  1.32 (0.26), residues: 983
  helix:  1.92 (0.21), residues: 636
  sheet: -0.75 (0.89), residues: 24
  loop : -1.14 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  35 
 TYR   0.014   0.002   TYR D 121 
 PHE   0.013   0.002   PHE D  65 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.006   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.20 (14864)
  covalent geometry    : angle       0.63946 /  0.36 (21353)
  hydrogen bonds       : bond        0.06595 /  4.57 (  811)
  hydrogen bonds       : angle       3.10026 /  2.27 ( 2062)
  metal coordination   : bond        0.00564 /  0.27 (    8)
  metal coordination   : angle       2.08233 /  1.17 (    9)
  link_TRANS           : bond        0.00049 /  0.02 (    2)
  link_TRANS           : angle       0.57067 /  0.27 (    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
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.376 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8012 (mt-10)
REVERT: C  118 LYS cc_start: 0.7897 (pttm) cc_final: 0.7133 (ptpp)
REVERT: D   35 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7837 (mt-10)
REVERT: H  112 SER cc_start: 0.9148 (t) cc_final: 0.8498 (m)
REVERT: L   78 ILE cc_start: 0.6139 (mp) cc_final: 0.5540 (tp)
  outliers start: 5
  outliers final: 4
  residues processed: 95
  average time/residue: 0.1575
  time to fit residues: 20.3897
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain L residue   88 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:    9.9990
   chunk 118 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.7380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.160843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.120588 restraints weight = 27227.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.33
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.0761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14874  Z= 0.140
  Angle     :  0.615   7.490  21368  Z= 0.350
  Chirality :  0.046   0.286   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.828 178.839   4332
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  8.41 %
    Favored  : 91.00 %
  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:  1.49 (0.26), residues: 983
  helix:  2.06 (0.21), residues: 636
  sheet: -0.67 (0.90), residues: 24
  loop : -1.11 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.010   0.002   PHE A  78 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.14 (14864)
  covalent geometry    : angle       0.61334 /  0.35 (21353)
  hydrogen bonds       : bond        0.06055 /  4.21 (  811)
  hydrogen bonds       : angle       3.07474 /  2.25 ( 2062)
  metal coordination   : bond        0.00511 /  0.23 (    8)
  metal coordination   : angle       1.92486 /  1.09 (    9)
  link_TRANS           : bond        0.00068 /  0.03 (    2)
  link_TRANS           : angle       1.00753 /  0.42 (    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
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.366 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7168 (mt-10)
REVERT: C  118 LYS cc_start: 0.7881 (pttm) cc_final: 0.7221 (ptpp)
REVERT: D   35 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7837 (mt-10)
REVERT: H   54 ILE cc_start: 0.9106 (tt) cc_final: 0.8840 (tt)
REVERT: H  112 SER cc_start: 0.9106 (t) cc_final: 0.8509 (m)
  outliers start: 5
  outliers final: 4
  residues processed: 96
  average time/residue: 0.1685
  time to fit residues: 21.7428
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain L residue   88 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.152107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.115494 restraints weight = 20269.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.85
r_work: 0.2739 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.0889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14874  Z= 0.221
  Angle     :  0.661   7.752  21368  Z= 0.369
  Chirality :  0.048   0.316   2419
  Planarity :  0.005   0.041   1688
  Dihedral  : 29.967 179.747   4332
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.46 %
    Favored  : 89.60 %
  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:  1.12 (0.26), residues: 983
  helix:  1.80 (0.20), residues: 636
  sheet: -0.65 (0.91), residues: 24
  loop : -1.34 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  35 
 TYR   0.015   0.002   TYR D 121 
 PHE   0.015   0.002   PHE D  65 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.007   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00494 /  0.22 (14864)
  covalent geometry    : angle       0.65998 /  0.37 (21353)
  hydrogen bonds       : bond        0.06951 /  4.80 (  811)
  hydrogen bonds       : angle       3.14995 /  2.30 ( 2062)
  metal coordination   : bond        0.00582 /  0.28 (    8)
  metal coordination   : angle       2.26419 /  1.29 (    9)
  link_TRANS           : bond        0.00020 /  0.01 (    2)
  link_TRANS           : angle       0.70998 /  0.34 (    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
  106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7456 (pt0)
REVERT: B   74 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: C  118 LYS cc_start: 0.7913 (pttm) cc_final: 0.7082 (ptpp)
REVERT: D   35 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7830 (mt-10)
REVERT: H   54 ILE cc_start: 0.9261 (tt) cc_final: 0.9029 (tt)
REVERT: H  112 SER cc_start: 0.9103 (t) cc_final: 0.8433 (m)
  outliers start: 8
  outliers final: 5
  residues processed: 102
  average time/residue: 0.1503
  time to fit residues: 21.0267
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain L residue   88 ILE
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:    0.5980
   chunk 96 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.8586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.162021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.116462 restraints weight = 19410.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.38
r_work: 0.2699 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (14 function evaluations)
r_final: 0.2619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  14874  Z= 0.148
  Angle     :  0.624   7.795  21368  Z= 0.353
  Chirality :  0.046   0.271   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.893 178.754   4332
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.05 %
    Favored  : 89.25 %
  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:  1.36 (0.26), residues: 983
  helix:  2.01 (0.21), residues: 636
  sheet: -0.63 (0.92), residues: 24
  loop : -1.28 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 131 
 TYR   0.011   0.001   TYR L  74 
 PHE   0.011   0.001   PHE F  61 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.005   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 (14864)
  covalent geometry    : angle       0.62317 /  0.35 (21353)
  hydrogen bonds       : bond        0.06082 /  4.23 (  811)
  hydrogen bonds       : angle       3.06683 /  2.24 ( 2062)
  metal coordination   : bond        0.00459 /  0.21 (    8)
  metal coordination   : angle       1.94323 /  1.11 (    9)
  link_TRANS           : bond        0.00157 /  0.08 (    2)
  link_TRANS           : angle       0.70466 /  0.33 (    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
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.344 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7881 (pttm) cc_final: 0.7121 (ptpp)
REVERT: D   35 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: H   54 ILE cc_start: 0.9240 (tt) cc_final: 0.8994 (tt)
REVERT: H  112 SER cc_start: 0.9128 (t) cc_final: 0.8484 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 95
  average time/residue: 0.1685
  time to fit residues: 21.5438
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   88 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.167574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.125622 restraints weight = 24204.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 1.77
r_work: 0.2617 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.0848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.143  14874  Z= 0.148
  Angle     :  0.616   7.569  21368  Z= 0.349
  Chirality :  0.046   0.275   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.899 179.429   4332
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.16 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.26), residues: 983
  helix:  2.07 (0.21), residues: 636
  sheet: -0.65 (0.92), residues: 24
  loop : -1.25 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  68 
 TYR   0.009   0.001   TYR D 121 
 PHE   0.010   0.001   PHE F  61 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.15 (14864)
  covalent geometry    : angle       0.61484 /  0.35 (21353)
  hydrogen bonds       : bond        0.06023 /  4.20 (  811)
  hydrogen bonds       : angle       3.02921 /  2.21 ( 2062)
  metal coordination   : bond        0.00504 /  0.23 (    8)
  metal coordination   : angle       1.94109 /  1.10 (    9)
  link_TRANS           : bond        0.00030 /  0.02 (    2)
  link_TRANS           : angle       0.73995 /  0.34 (    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
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.416 
Fit side-chains
REVERT: C   92 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8881 (mp0)
REVERT: C  118 LYS cc_start: 0.7885 (pttm) cc_final: 0.7082 (ptpp)
REVERT: D   35 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7872 (mt-10)
REVERT: H   54 ILE cc_start: 0.9236 (tt) cc_final: 0.9000 (tt)
REVERT: H  112 SER cc_start: 0.9109 (t) cc_final: 0.8445 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1733
  time to fit residues: 22.5785
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain L residue   88 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 92 optimal weight:    9.9990
   chunk 113 optimal weight:    0.2980
   chunk 51 optimal weight:    0.7980
   chunk 116 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.0184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.168639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.124023 restraints weight = 26650.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.79
r_work: 0.2636 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2565
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2565 r_free = 0.2565    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2565 r_free = 0.2565    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.0852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14874  Z= 0.152
  Angle     :  0.612   7.399  21368  Z= 0.347
  Chirality :  0.045   0.280   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.895 179.292   4332
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.81 %
    Favored  : 89.25 %
  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:  1.46 (0.26), residues: 983
  helix:  2.08 (0.21), residues: 636
  sheet: -0.58 (0.94), residues: 24
  loop : -1.24 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  35 
 TYR   0.009   0.001   TYR D 121 
 PHE   0.010   0.002   PHE F  61 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.15 (14864)
  covalent geometry    : angle       0.61044 /  0.35 (21353)
  hydrogen bonds       : bond        0.05976 /  4.17 (  811)
  hydrogen bonds       : angle       3.01806 /  2.20 ( 2062)
  metal coordination   : bond        0.00462 /  0.21 (    8)
  metal coordination   : angle       1.97126 /  1.11 (    9)
  link_TRANS           : bond        0.00074 /  0.04 (    2)
  link_TRANS           : angle       0.64066 /  0.29 (    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
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.371 
Fit side-chains
REVERT: C   92 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8926 (mp0)
REVERT: C  118 LYS cc_start: 0.7885 (pttm) cc_final: 0.7085 (ptpp)
REVERT: D   35 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: H   54 ILE cc_start: 0.9253 (tt) cc_final: 0.9012 (tt)
REVERT: H  112 SER cc_start: 0.9148 (t) cc_final: 0.8501 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1698
  time to fit residues: 22.7112
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   88 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 119 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0980
   chunk 19 optimal weight:    0.3980
   chunk 97 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 72 optimal weight:   20.0000
   overall best weight:    0.7982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.168882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.123300 restraints weight = 24470.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 1.53
r_work: 0.2682 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.2611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  14874  Z= 0.142
  Angle     :  0.608   7.386  21368  Z= 0.345
  Chirality :  0.045   0.278   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.890 179.163   4332
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.93 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.26), residues: 983
  helix:  2.12 (0.21), residues: 636
  sheet: -0.60 (0.94), residues: 24
  loop : -1.23 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  92 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.010   0.001   PHE F  61 
 TRP   0.007   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.14 (14864)
  covalent geometry    : angle       0.60671 /  0.35 (21353)
  hydrogen bonds       : bond        0.05897 /  4.12 (  811)
  hydrogen bonds       : angle       3.01402 /  2.20 ( 2062)
  metal coordination   : bond        0.00476 /  0.22 (    8)
  metal coordination   : angle       1.94696 /  1.10 (    9)
  link_TRANS           : bond        0.00068 /  0.03 (    2)
  link_TRANS           : angle       0.66029 /  0.30 (    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
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.368 
Fit side-chains
REVERT: C   92 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8846 (mp0)
REVERT: C  118 LYS cc_start: 0.7873 (pttm) cc_final: 0.7100 (ptpp)
REVERT: D   35 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7881 (mt-10)
REVERT: H   54 ILE cc_start: 0.9241 (tt) cc_final: 0.9003 (tt)
REVERT: H  112 SER cc_start: 0.9137 (t) cc_final: 0.8491 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1706
  time to fit residues: 22.7425
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain K residue   60 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   88 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 25 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 98 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9990
   chunk 92 optimal weight:   10.0000
   chunk 115 optimal weight:    9.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5578

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.168347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.124844 restraints weight = 19010.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 1.18
r_work: 0.2766 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.0847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.063  14874  Z= 0.131
  Angle     :  0.601   7.298  21368  Z= 0.343
  Chirality :  0.045   0.272   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.880 178.966   4332
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.81 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.27), residues: 983
  helix:  2.16 (0.21), residues: 636
  sheet: -0.59 (0.94), residues: 24
  loop : -1.21 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  35 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.010   0.001   PHE F  61 
 TRP   0.007   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.13 (14864)
  covalent geometry    : angle       0.60009 /  0.34 (21353)
  hydrogen bonds       : bond        0.05794 /  4.05 (  811)
  hydrogen bonds       : angle       3.00331 /  2.19 ( 2062)
  metal coordination   : bond        0.00430 /  0.19 (    8)
  metal coordination   : angle       1.92516 /  1.09 (    9)
  link_TRANS           : bond        0.00093 /  0.05 (    2)
  link_TRANS           : angle       0.78349 /  0.34 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3040.18 seconds
wall clock time: 52 minutes 41.97 seconds (3161.97 seconds total)