Starting phenix.real_space_refine
on Sat Aug 23 17:32:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smw_40604/08_2025/8smw_40604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smw_40604/08_2025/8smw_40604.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2025/8smw_40604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2025/8smw_40604.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2025/8smw_40604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smw_40604/08_2025/8smw_40604.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.105
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7891      2.51       5
     N    2608      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13998
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      34.563  67.474  43.721  1.00 33.88           S
  ATOM  12446  SG  CYS K  51      32.713  64.181  43.621  1.00 29.69           S
  ATOM  12470  SG  CYS K  54      34.556  65.439  40.531  1.00 35.60           S
  ATOM  12187  SG  CYS K  16      22.929  63.352  48.998  1.00 58.51           S
  ATOM  12205  SG  CYS K  19      20.440  61.444  50.962  1.00 60.46           S
  ATOM  12335  SG  CYS K  36      23.193  63.501  52.800  1.00 47.61           S
  ATOM  12357  SG  CYS K  39      24.103  60.352  51.278  1.00 48.10           S

  Time building chain proxies: 3.47, per 1000 atoms: 0.25
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 130.144, 128.816, 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: 1.02
  Conformation dependent library (CDL) restraints added in 426.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  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  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


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

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 12 sheets defined
      64.2% alpha, 4.5% beta
      136 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.615A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.783A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.043A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.504A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.553A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.749A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.692A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 4.069A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.690A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.851A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.618A  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: 3.579A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.571A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.549A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.760A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 3.841A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.661A  pdb=" N   TRP K  77 " --> pdb=" O   ASN K  73 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 4.377A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LYS K  89 " --> pdb=" O   PRO K  85 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.811A  pdb=" N   ARG L   5 " --> pdb=" O   MET L   1 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP L  16 " --> pdb=" O   ASP L  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.568A  pdb=" N   LEU L 110 " --> pdb=" O   ILE L 106 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP L 111 " --> pdb=" O   ALA L 107 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.548A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LYS L 144 " --> pdb=" O   GLU L 140 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.940A  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
      removed outlier: 6.625A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.542A  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: 6.860A  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: 7.101A  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: 7.714A  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
      removed outlier: 3.536A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    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

    464 hydrogen bonds defined for protein.
    1374 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2994
        1.33 -     1.46: 4511
        1.46 -     1.58: 6726
        1.58 -     1.70: 586
        1.70 -     1.82: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.44e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" CG  PRO L  61 "
       pdb=" CD  PRO L  61 "
    ideal  model  delta    sigma   weight residual
    1.512  1.483  0.029 2.70e-02 1.37e+03 1.15e+00
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.45e-01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 7.88e-01
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 20944
        1.69 -     3.39: 390
        3.39 -     5.08: 16
        5.08 -     6.77: 2
        6.77 -     8.46: 1
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" CB  MET L  30 "
        pdb=" CG  MET L  30 "
        pdb=" SD  MET L  30 "
      ideal   model   delta    sigma   weight residual
     112.70  121.16   -8.46 3.00e+00 1.11e-01 7.96e+00
  angle pdb=" C3'  DG J -70 "
        pdb=" C2'  DG J -70 "
        pdb=" C1'  DG J -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.42   -3.82 1.50e+00 4.44e-01 6.47e+00
  angle pdb=" C   ALA D 110 "
        pdb=" N   VAL D 111 "
        pdb=" CA  VAL D 111 "
      ideal   model   delta    sigma   weight residual
     120.60  123.59   -2.99 1.29e+00 6.01e-01 5.38e+00
  angle pdb=" N   ASN G  73 "
        pdb=" CA  ASN G  73 "
        pdb=" C   ASN G  73 "
      ideal   model   delta    sigma   weight residual
     112.59  109.81    2.78 1.22e+00 6.72e-01 5.20e+00
  angle pdb=" N   ASN L   7 "
        pdb=" CA  ASN L   7 "
        pdb=" CB  ASN L   7 "
      ideal   model   delta    sigma   weight residual
     110.12  113.41   -3.29 1.47e+00 4.63e-01 5.00e+00
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 6856
       35.68 -    71.37: 1354
       71.37 -   107.05: 18
      107.05 -   142.74: 0
      142.74 -   178.42: 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
    -140.00   38.42 -178.42     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   71.12  148.88     1      3.50e+01 8.16e-04 1.45e+01
  dihedral pdb=" CG  ARG F  67 "
           pdb=" CD  ARG F  67 "
           pdb=" NE  ARG F  67 "
           pdb=" CZ  ARG F  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.35  -44.35     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1541
       0.026 -    0.052: 591
       0.052 -    0.078: 195
       0.078 -    0.105: 62
       0.105 -    0.131: 30
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CA  VAL K  24 "
            pdb=" N   VAL K  24 "
            pdb=" C   VAL K  24 "
            pdb=" CB  VAL K  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CB  ILE K   8 "
            pdb=" CA  ILE K   8 "
            pdb=" CG1 ILE K   8 "
            pdb=" CG2 ILE K   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.13 2.00e-01 2.50e+01 4.10e-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   1.13e-02 3.50e+00
        pdb=" N9   DA I -35 "    0.024 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 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.022 2.00e-02 2.50e+03   9.01e-03 2.44e+00
        pdb=" N9   DG I  47 "    0.019 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.005 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=" CA  ALA D 107 "   -0.007 2.00e-02 2.50e+03   1.39e-02 1.94e+00
        pdb=" C   ALA D 107 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ALA D 107 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   LYS D 108 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 368
        2.68 -     3.23: 11841
        3.23 -     3.79: 24083
        3.79 -     4.34: 32108
        4.34 -     4.90: 47074
  Nonbonded interactions: 115474
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.124 2.496
  nonbonded pdb=" O   ASN G  73 "
            pdb=" ND2 ASN G  73 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.305 3.040
  ... (remaining 115469 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.890
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14874  Z= 0.147
  Angle     :  0.535   8.463  21368  Z= 0.315
  Chirality :  0.034   0.131   2419
  Planarity :  0.004   0.035   1688
  Dihedral  : 26.233 178.423   6336
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.27), residues: 983
  helix:  2.18 (0.21), residues: 625
  sheet:  0.52 (1.01), residues: 24
  loop : -0.86 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 125 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.009   0.001   PHE L  62 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS L   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (14864)
  covalent geometry    : angle       0.52851 (21353)
  hydrogen bonds       : bond        0.11039 (  813)
  hydrogen bonds       : angle       4.07863 ( 2068)
  metal coordination   : bond        0.00473 (    8)
  metal coordination   : angle       4.06902 (    9)
  link_TRANS           : bond        0.00156 (    2)
  link_TRANS           : angle       0.56251 (    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
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.339 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7713 (m-40) cc_final: 0.7270 (t0)
REVERT: D   99 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7445 (mtm-85)
REVERT: H   46 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8435 (mmtt)
REVERT: H   79 ARG cc_start: 0.8895 (ttm110) cc_final: 0.8512 (ttm170)
REVERT: H   99 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7496 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1877
  time to fit residues: 27.0084
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0370
   chunk 51 optimal weight:    0.3980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
D  47 GLN
L   7 ASN
L  92 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.158925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.104531 restraints weight = 30055.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.96
r_work: 0.2734 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.0432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.148
  Angle     :  0.538   7.374  21368  Z= 0.315
  Chirality :  0.034   0.134   2419
  Planarity :  0.004   0.035   1688
  Dihedral  : 29.234 178.407   4332
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  4.44 %
    Favored  : 94.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.27), residues: 983
  helix:  2.47 (0.21), residues: 627
  sheet:  0.52 (1.01), residues: 24
  loop : -0.91 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 125 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.009   0.001   PHE L  62 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (14864)
  covalent geometry    : angle       0.53150 (21353)
  hydrogen bonds       : bond        0.05171 (  813)
  hydrogen bonds       : angle       3.33120 ( 2068)
  metal coordination   : bond        0.00437 (    8)
  metal coordination   : angle       3.97739 (    9)
  link_TRANS           : bond        0.00056 (    2)
  link_TRANS           : angle       0.32595 (    6)

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

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.379 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7490 (m-40) cc_final: 0.6795 (t0)
REVERT: D   99 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7704 (mtm-85)
REVERT: H   46 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8455 (mmtt)
REVERT: L    7 ASN cc_start: 0.8566 (m-40) cc_final: 0.8265 (m110)
REVERT: L   30 MET cc_start: 0.5834 (mmm) cc_final: 0.5579 (mmm)
REVERT: L  147 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6022 (ptp)
  outliers start: 6
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1578
  time to fit residues: 22.6226
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  123 ILE
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 117 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 85 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 110 optimal weight:    0.0060
   overall best weight:    1.0600

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
B  93 GLN
L  92 GLN
L 135 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.153223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.097622 restraints weight = 25774.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 1.78
r_work: 0.2654 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.0817

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= 0.171
  Angle     :  0.545   7.988  21368  Z= 0.319
  Chirality :  0.035   0.132   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.194 178.190   4332
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  7.24 %
    Favored  : 92.06 %
  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 aren not related in a simple way.
  whole:  2.01 (0.27), residues: 983
  helix:  2.52 (0.21), residues: 627
  sheet:  0.54 (1.04), residues: 24
  loop : -1.03 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  99 
 TYR   0.009   0.001   TYR G  50 
 PHE   0.010   0.002   PHE D  65 
 TRP   0.010   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (14864)
  covalent geometry    : angle       0.53830 (21353)
  hydrogen bonds       : bond        0.05339 (  813)
  hydrogen bonds       : angle       3.11690 ( 2068)
  metal coordination   : bond        0.00544 (    8)
  metal coordination   : angle       4.19454 (    9)
  link_TRANS           : bond        0.00030 (    2)
  link_TRANS           : angle       0.22397 (    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
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.284 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7556 (m-40) cc_final: 0.6950 (t0)
REVERT: D   99 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7720 (mtm-85)
REVERT: G   73 ASN cc_start: 0.8485 (t0) cc_final: 0.8265 (t0)
REVERT: H   99 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7853 (mtm-85)
REVERT: L   30 MET cc_start: 0.5662 (mmm) cc_final: 0.5353 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1526
  time to fit residues: 19.8350
Evaluate side-chains
  93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0050
   chunk 27 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 119 optimal weight:    7.9990
   chunk 106 optimal weight:    0.0770
   chunk 112 optimal weight:    5.9990
   overall best weight:    0.4752

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
L  92 GLN
L 135 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.155689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.101129 restraints weight = 20697.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.53
r_work: 0.2726 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.0835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.140
  Angle     :  0.527   7.645  21368  Z= 0.310
  Chirality :  0.034   0.130   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.136 178.484   4332
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.06 %
    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 aren not related in a simple way.
  whole:  2.18 (0.27), residues: 983
  helix:  2.66 (0.21), residues: 626
  sheet:  0.57 (1.05), residues: 24
  loop : -0.96 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 129 
 TYR   0.008   0.001   TYR H 121 
 PHE   0.009   0.001   PHE L  62 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (14864)
  covalent geometry    : angle       0.52051 (21353)
  hydrogen bonds       : bond        0.04844 (  813)
  hydrogen bonds       : angle       3.04830 ( 2068)
  metal coordination   : bond        0.00472 (    8)
  metal coordination   : angle       3.93064 (    9)
  link_TRANS           : bond        0.00093 (    2)
  link_TRANS           : angle       0.18288 (    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
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.309 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7367 (m-40) cc_final: 0.6870 (t0)
REVERT: D   99 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7698 (mtm-85)
REVERT: G   73 ASN cc_start: 0.8457 (t0) cc_final: 0.8183 (t0)
REVERT: H   47 GLN cc_start: 0.8513 (mt0) cc_final: 0.8233 (mt0)
REVERT: H   99 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7811 (mtm-85)
REVERT: L   30 MET cc_start: 0.5433 (mmm) cc_final: 0.5083 (mmm)
REVERT: L  147 MET cc_start: 0.6633 (ptp) cc_final: 0.6045 (pmm)
  outliers start: 8
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1531
  time to fit residues: 19.9840
Evaluate side-chains
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 61 optimal weight:    0.2980
   chunk 57 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 113 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
L  92 GLN
L 135 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.156922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.102392 restraints weight = 29136.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.96
r_work: 0.2696 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.146
  Angle     :  0.521   7.188  21368  Z= 0.307
  Chirality :  0.034   0.133   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.091 178.479   4332
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.88 %
    Favored  : 90.19 %
  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 aren not related in a simple way.
  whole:  2.22 (0.27), residues: 983
  helix:  2.68 (0.21), residues: 627
  sheet:  0.61 (1.05), residues: 24
  loop : -0.93 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 136 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.011   0.001   PHE L  50 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14864)
  covalent geometry    : angle       0.51538 (21353)
  hydrogen bonds       : bond        0.04786 (  813)
  hydrogen bonds       : angle       2.96974 ( 2068)
  metal coordination   : bond        0.00494 (    8)
  metal coordination   : angle       3.82874 (    9)
  link_TRANS           : bond        0.00033 (    2)
  link_TRANS           : angle       0.21178 (    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
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.269 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7308 (m-40) cc_final: 0.6813 (t0)
REVERT: D   99 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7685 (mtm-85)
REVERT: G   73 ASN cc_start: 0.8497 (t0) cc_final: 0.8185 (t0)
REVERT: H   99 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.7951 (mtm-85)
REVERT: L   30 MET cc_start: 0.5359 (mmm) cc_final: 0.4976 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 95
  average time/residue: 0.1574
  time to fit residues: 19.7898
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  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 72 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0050
   chunk 36 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.0598

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
H  47 GLN
L  92 GLN
L 135 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.153314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.098172 restraints weight = 21029.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.45
r_work: 0.2711 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1079

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= 0.168
  Angle     :  0.538   7.656  21368  Z= 0.314
  Chirality :  0.035   0.138   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.272 178.229   4332
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.11 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.27), residues: 983
  helix:  2.62 (0.21), residues: 626
  sheet:  0.54 (1.04), residues: 24
  loop : -0.95 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  99 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.017   0.002   PHE L  50 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (14864)
  covalent geometry    : angle       0.53136 (21353)
  hydrogen bonds       : bond        0.05268 (  813)
  hydrogen bonds       : angle       3.02292 ( 2068)
  metal coordination   : bond        0.00528 (    8)
  metal coordination   : angle       4.12224 (    9)
  link_TRANS           : bond        0.00028 (    2)
  link_TRANS           : angle       0.24914 (    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
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.7417 (t0) cc_final: 0.7165 (t0)
REVERT: C   73 ASN cc_start: 0.7390 (m-40) cc_final: 0.7018 (t0)
REVERT: D   99 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.7802 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8589 (mm-30)
REVERT: G   73 ASN cc_start: 0.8642 (t0) cc_final: 0.8309 (t0)
REVERT: H   99 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.7988 (mtm-85)
REVERT: L    7 ASN cc_start: 0.8823 (m110) cc_final: 0.8613 (m110)
REVERT: L   30 MET cc_start: 0.5837 (mmm) cc_final: 0.5455 (mmm)
REVERT: L  147 MET cc_start: 0.6715 (ptp) cc_final: 0.6401 (ptp)
  outliers start: 7
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1495
  time to fit residues: 17.7178
Evaluate side-chains
  90 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
L  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.154797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.100094 restraints weight = 20499.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 1.55
r_work: 0.2683 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1152

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= 0.163
  Angle     :  0.530   7.550  21368  Z= 0.310
  Chirality :  0.035   0.136   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.221 178.387   4332
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.70 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.27), residues: 983
  helix:  2.63 (0.21), residues: 626
  sheet:  0.48 (1.04), residues: 24
  loop : -0.94 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 131 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.014   0.002   PHE L  50 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (14864)
  covalent geometry    : angle       0.52406 (21353)
  hydrogen bonds       : bond        0.05035 (  813)
  hydrogen bonds       : angle       2.99121 ( 2068)
  metal coordination   : bond        0.00510 (    8)
  metal coordination   : angle       3.99431 (    9)
  link_TRANS           : bond        0.00038 (    2)
  link_TRANS           : angle       0.21553 (    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
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.7613 (t0) cc_final: 0.7375 (t0)
REVERT: C   73 ASN cc_start: 0.7276 (m-40) cc_final: 0.6987 (t0)
REVERT: D   99 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.7848 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8681 (mm-30)
REVERT: G   73 ASN cc_start: 0.8517 (t0) cc_final: 0.8140 (t0)
REVERT: H   99 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.8012 (mtm-85)
REVERT: L    7 ASN cc_start: 0.8806 (m110) cc_final: 0.8570 (m110)
REVERT: L   30 MET cc_start: 0.5899 (mmm) cc_final: 0.5515 (mmm)
REVERT: L  147 MET cc_start: 0.6685 (ptp) cc_final: 0.6450 (ptp)
  outliers start: 7
  outliers final: 6
  residues processed: 93
  average time/residue: 0.1616
  time to fit residues: 20.2675
Evaluate side-chains
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0970
   chunk 21 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0070
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
L  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.155494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.101471 restraints weight = 26406.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.82
r_work: 0.2683 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.141
  Angle     :  0.525   8.252  21368  Z= 0.308
  Chirality :  0.034   0.151   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.207 178.587   4332
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.51 %
    Favored  : 88.90 %
  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 aren not related in a simple way.
  whole:  2.24 (0.27), residues: 983
  helix:  2.70 (0.21), residues: 626
  sheet:  0.50 (1.04), residues: 24
  loop : -0.92 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  99 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.010   0.001   PHE L  50 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (14864)
  covalent geometry    : angle       0.51911 (21353)
  hydrogen bonds       : bond        0.04792 (  813)
  hydrogen bonds       : angle       2.98731 ( 2068)
  metal coordination   : bond        0.00443 (    8)
  metal coordination   : angle       3.87351 (    9)
  link_TRANS           : bond        0.00068 (    2)
  link_TRANS           : angle       0.19826 (    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
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.7607 (t0) cc_final: 0.7363 (t0)
REVERT: C   73 ASN cc_start: 0.7231 (m-40) cc_final: 0.6951 (t0)
REVERT: D   99 ARG cc_start: 0.8346 (mtt-85) cc_final: 0.7853 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8601 (mm-30)
REVERT: G   73 ASN cc_start: 0.8504 (t0) cc_final: 0.8114 (t0)
REVERT: H   99 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8012 (mtm-85)
REVERT: L   30 MET cc_start: 0.5871 (mmm) cc_final: 0.5486 (mmm)
REVERT: L  147 MET cc_start: 0.6702 (ptp) cc_final: 0.6482 (ptp)
  outliers start: 5
  outliers final: 4
  residues processed: 91
  average time/residue: 0.1729
  time to fit residues: 20.9375
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  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 92 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
L  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.149871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.110053 restraints weight = 29662.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.65
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.153
  Angle     :  0.526   8.510  21368  Z= 0.308
  Chirality :  0.034   0.135   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.189 178.423   4332
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.75 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.27), residues: 983
  helix:  2.66 (0.21), residues: 626
  sheet:  0.54 (1.05), residues: 24
  loop : -0.93 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  99 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.012   0.001   PHE L  50 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (14864)
  covalent geometry    : angle       0.51991 (21353)
  hydrogen bonds       : bond        0.04874 (  813)
  hydrogen bonds       : angle       2.98165 ( 2068)
  metal coordination   : bond        0.00470 (    8)
  metal coordination   : angle       3.91024 (    9)
  link_TRANS           : bond        0.00042 (    2)
  link_TRANS           : angle       0.20183 (    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
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.6984 (t0) cc_final: 0.6760 (t0)
REVERT: D   99 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7579 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: G   73 ASN cc_start: 0.8237 (t0) cc_final: 0.7893 (t0)
REVERT: H   99 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7491 (mtm-85)
REVERT: L   30 MET cc_start: 0.6182 (mmm) cc_final: 0.5898 (mmm)
REVERT: L  147 MET cc_start: 0.5809 (ptp) cc_final: 0.5549 (ptp)
  outliers start: 6
  outliers final: 5
  residues processed: 92
  average time/residue: 0.1853
  time to fit residues: 22.8111
Evaluate side-chains
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0670
   chunk 119 optimal weight:    0.0870
   chunk 43 optimal weight:    0.3980
   chunk 114 optimal weight:    0.0030
   chunk 19 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.2706

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  25 ASN
L  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.151090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.110235 restraints weight = 27398.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.26
r_work: 0.2916 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14874  Z= 0.134
  Angle     :  0.521   8.933  21368  Z= 0.308
  Chirality :  0.034   0.131   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.154 178.768   4332
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.75 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.27), residues: 983
  helix:  2.73 (0.21), residues: 627
  sheet:  0.58 (1.05), residues: 24
  loop : -0.90 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 116 
 TYR   0.007   0.001   TYR G  57 
 PHE   0.012   0.001   PHE L  50 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.002   0.000   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (14864)
  covalent geometry    : angle       0.51595 (21353)
  hydrogen bonds       : bond        0.04542 (  813)
  hydrogen bonds       : angle       2.99411 ( 2068)
  metal coordination   : bond        0.00436 (    8)
  metal coordination   : angle       3.74264 (    9)
  link_TRANS           : bond        0.00106 (    2)
  link_TRANS           : angle       0.16548 (    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
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.7608 (t0) cc_final: 0.7365 (t0)
REVERT: D   99 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.7878 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8584 (mm-30)
REVERT: G   73 ASN cc_start: 0.8488 (t0) cc_final: 0.8114 (t0)
REVERT: L   30 MET cc_start: 0.5906 (mmm) cc_final: 0.5531 (mmm)
REVERT: L  147 MET cc_start: 0.6617 (ptp) cc_final: 0.6369 (ptp)
  outliers start: 6
  outliers final: 4
  residues processed: 92
  average time/residue: 0.1767
  time to fit residues: 21.8594
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  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue  100 SER
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:    0.0980
   chunk 25 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  73 ASN
L  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.151803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.111361 restraints weight = 21037.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.59
r_work: 0.2719 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14874  Z= 0.140
  Angle     :  0.515   8.481  21368  Z= 0.303
  Chirality :  0.033   0.131   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.074 178.637   4332
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.10 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.27), residues: 983
  helix:  2.72 (0.21), residues: 630
  sheet:  0.59 (1.05), residues: 24
  loop : -0.85 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 136 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.011   0.001   PHE L  50 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (14864)
  covalent geometry    : angle       0.50941 (21353)
  hydrogen bonds       : bond        0.04498 (  813)
  hydrogen bonds       : angle       2.93942 ( 2068)
  metal coordination   : bond        0.00441 (    8)
  metal coordination   : angle       3.77941 (    9)
  link_TRANS           : bond        0.00066 (    2)
  link_TRANS           : angle       0.16228 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2980.16 seconds
wall clock time: 51 minutes 39.30 seconds (3099.30 seconds total)