Starting phenix.real_space_refine
on Thu Jul 31 16:48:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smw_40604/07_2025/8smw_40604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smw_40604/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2025/8smw_40604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2025/8smw_40604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2025/8smw_40604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smw_40604/07_2025/8smw_40604.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.80, per 1000 atoms: 0.63
  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: 2.95
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  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: 6.11
  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: 5.40

  Time building geometry restraints manager: 3.61 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:             1.150
  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:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     39.620
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.070
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.720
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS L   0 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.007   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00156 (    2)
  link_TRANS           : angle       0.56251 (    6)
  hydrogen bonds       : bond        0.11039 (  813)
  hydrogen bonds       : angle       4.07863 ( 2068)
  metal coordination   : bond        0.00473 (    8)
  metal coordination   : angle       4.06902 (    9)
  covalent geometry    : bond        0.00322 (14864)
  covalent geometry    : angle       0.52851 (21353)

*********************** 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  : 1.107 
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: 0.4000
  time to fit residues: 57.9338
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  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 110 optimal weight:    0.6980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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
G  24 GLN
L   7 ASN
L  92 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.151695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.100726 restraints weight = 20366.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 1.44
r_work: 0.2733 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.0735

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= 0.176
  Angle     :  0.556   7.982  21368  Z= 0.324
  Chirality :  0.035   0.133   2419
  Planarity :  0.004   0.035   1688
  Dihedral  : 29.230 178.129   4332
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  4.91 %
    Favored  : 94.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.27), residues: 983
  helix:  2.41 (0.21), residues: 627
  sheet:  0.59 (1.05), residues: 24
  loop : -1.01 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.004   0.001   HIS H  49 
 PHE   0.010   0.002   PHE L  62 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.004   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00052 (    2)
  link_TRANS           : angle       0.25016 (    6)
  hydrogen bonds       : bond        0.05430 (  813)
  hydrogen bonds       : angle       3.22172 ( 2068)
  metal coordination   : bond        0.00543 (    8)
  metal coordination   : angle       4.23347 (    9)
  covalent geometry    : bond        0.00400 (14864)
  covalent geometry    : angle       0.54898 (21353)

*********************** 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
  110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 1.028 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7565 (m-40) cc_final: 0.6914 (t0)
REVERT: D   99 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.7831 (mtm-85)
REVERT: H   99 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.7679 (mtm180)
REVERT: L    7 ASN cc_start: 0.8677 (m-40) cc_final: 0.8211 (m110)
REVERT: L   30 MET cc_start: 0.5815 (mmm) cc_final: 0.5530 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 106
  average time/residue: 0.3642
  time to fit residues: 51.5313
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain L residue   69 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0370
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 101 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 120 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.6658

-------------------------------------------------------------------------------
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
G  24 GLN
L  92 GLN
L 135 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.153302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.102843 restraints weight = 21682.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 1.51
r_work: 0.2826 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2588 r_free = 0.2588    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2588 r_free = 0.2588    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.0842

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= 0.146
  Angle     :  0.525   7.255  21368  Z= 0.309
  Chirality :  0.034   0.128   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.098 178.462   4332
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  7.94 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.27), residues: 983
  helix:  2.61 (0.21), residues: 626
  sheet:  0.50 (1.04), residues: 24
  loop : -0.96 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS H  49 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.002   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00050 (    2)
  link_TRANS           : angle       0.22569 (    6)
  hydrogen bonds       : bond        0.04826 (  813)
  hydrogen bonds       : angle       3.03253 ( 2068)
  metal coordination   : bond        0.00464 (    8)
  metal coordination   : angle       3.97619 (    9)
  covalent geometry    : bond        0.00320 (14864)
  covalent geometry    : angle       0.51888 (21353)

*********************** 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
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.997 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7410 (m-40) cc_final: 0.6912 (t0)
REVERT: D   99 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.7844 (mtm-85)
REVERT: H   99 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.7732 (mtm180)
REVERT: L   30 MET cc_start: 0.5764 (mmm) cc_final: 0.5448 (mmm)
  outliers start: 6
  outliers final: 5
  residues processed: 98
  average time/residue: 0.3687
  time to fit residues: 48.2235
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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 G residue   24 GLN
Chi-restraints excluded: chain L residue   69 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 120 optimal weight:    5.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.151813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.102544 restraints weight = 27195.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.81
r_work: 0.2697 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.0951

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= 0.158
  Angle     :  0.529   7.561  21368  Z= 0.310
  Chirality :  0.034   0.133   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.162 178.348   4332
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  8.41 %
    Favored  : 90.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.27), residues: 983
  helix:  2.60 (0.21), residues: 626
  sheet:  0.59 (1.05), residues: 24
  loop : -0.97 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.011   0.001   PHE L  50 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.002   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00035 (    2)
  link_TRANS           : angle       0.21188 (    6)
  hydrogen bonds       : bond        0.04992 (  813)
  hydrogen bonds       : angle       3.01925 ( 2068)
  metal coordination   : bond        0.00494 (    8)
  metal coordination   : angle       4.03750 (    9)
  covalent geometry    : bond        0.00354 (14864)
  covalent geometry    : angle       0.52250 (21353)

*********************** 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
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.102 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7364 (m-40) cc_final: 0.6933 (t0)
REVERT: D   99 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.7778 (mtm-85)
REVERT: H   99 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7593 (mtm180)
REVERT: K   46 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8304 (ttmm)
REVERT: L   30 MET cc_start: 0.5844 (mmm) cc_final: 0.5508 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 93
  average time/residue: 0.3659
  time to fit residues: 45.8742
Evaluate side-chains
  91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
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  106 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.151040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.102106 restraints weight = 26179.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.83
r_work: 0.2688 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    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 = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1103

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     :  0.539   7.677  21368  Z= 0.315
  Chirality :  0.035   0.136   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.270 178.317   4332
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.35 %
    Favored  : 89.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.27), residues: 983
  helix:  2.57 (0.21), residues: 626
  sheet:  0.48 (1.04), residues: 24
  loop : -0.98 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.010   0.002   PHE D  65 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.003   0.000   ARG L 131 

Details of bonding type rmsd
  link_TRANS           : bond        0.00043 (    2)
  link_TRANS           : angle       0.23898 (    6)
  hydrogen bonds       : bond        0.05253 (  813)
  hydrogen bonds       : angle       3.03672 ( 2068)
  metal coordination   : bond        0.00552 (    8)
  metal coordination   : angle       4.14480 (    9)
  covalent geometry    : bond        0.00383 (14864)
  covalent geometry    : angle       0.53206 (21353)

*********************** 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
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.981 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7318 (m-40) cc_final: 0.6943 (t0)
REVERT: D   99 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.7788 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8585 (mm-30)
REVERT: H   99 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7555 (mtm180)
REVERT: K   46 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8302 (ttmm)
REVERT: L   30 MET cc_start: 0.5939 (mmm) cc_final: 0.5590 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 88
  average time/residue: 0.3596
  time to fit residues: 42.8310
Evaluate side-chains
  89 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 120 optimal weight:    0.0980
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0370
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.4858

-------------------------------------------------------------------------------
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   7 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.154694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.101356 restraints weight = 25952.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.77
r_work: 0.2701 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    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 = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1112

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= 0.138
  Angle     :  0.520   6.948  21368  Z= 0.306
  Chirality :  0.034   0.133   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.202 178.533   4332
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.75 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.27), residues: 983
  helix:  2.64 (0.21), residues: 628
  sheet:  0.49 (1.04), residues: 24
  loop : -0.90 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.007   0.001   TYR F  51 
 ARG   0.003   0.000   ARG L 131 

Details of bonding type rmsd
  link_TRANS           : bond        0.00098 (    2)
  link_TRANS           : angle       0.15935 (    6)
  hydrogen bonds       : bond        0.04776 (  813)
  hydrogen bonds       : angle       3.00358 ( 2068)
  metal coordination   : bond        0.00494 (    8)
  metal coordination   : angle       3.86316 (    9)
  covalent geometry    : bond        0.00292 (14864)
  covalent geometry    : angle       0.51392 (21353)

*********************** 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
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 1.099 
Fit side-chains
REVERT: D   99 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7852 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: H   99 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.7592 (mtm180)
REVERT: L   30 MET cc_start: 0.6051 (mmm) cc_final: 0.5669 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 93
  average time/residue: 0.3696
  time to fit residues: 46.0505
Evaluate side-chains
  90 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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
G  24 GLN
H  47 GLN
L   7 ASN
L  92 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.150547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.110175 restraints weight = 27200.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.25
r_work: 0.2669 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    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 = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1149

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     :  0.519   7.872  21368  Z= 0.306
  Chirality :  0.034   0.134   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.141 178.501   4332
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.51 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.27), residues: 983
  helix:  2.66 (0.21), residues: 629
  sheet:  0.54 (1.04), residues: 24
  loop : -0.90 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS H  49 
 PHE   0.014   0.001   PHE L  50 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.001   0.000   ARG F  40 

Details of bonding type rmsd
  link_TRANS           : bond        0.00063 (    2)
  link_TRANS           : angle       0.17739 (    6)
  hydrogen bonds       : bond        0.04741 (  813)
  hydrogen bonds       : angle       2.96444 ( 2068)
  metal coordination   : bond        0.00478 (    8)
  metal coordination   : angle       3.82635 (    9)
  covalent geometry    : bond        0.00323 (14864)
  covalent geometry    : angle       0.51331 (21353)

*********************** 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: 9
    poor density    : 88
  time to evaluate  : 1.164 
Fit side-chains
REVERT: D   99 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7904 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8703 (mm-30)
REVERT: H   99 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.7673 (mtm180)
REVERT: L    7 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8407 (m110)
REVERT: L   30 MET cc_start: 0.6003 (mmm) cc_final: 0.5631 (mmm)
  outliers start: 9
  outliers final: 6
  residues processed: 92
  average time/residue: 0.3689
  time to fit residues: 45.7256
Evaluate side-chains
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
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 G residue   24 GLN
Chi-restraints excluded: chain L residue    7 ASN
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 10 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0050
   chunk 93 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.1596

-------------------------------------------------------------------------------
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   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 = 0.3542 r_free = 0.3542 target = 0.148687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.107714 restraints weight = 26348.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.20
r_work: 0.2602 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2583 r_free = 0.2583    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2583 r_free = 0.2583    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1188

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= 0.175
  Angle     :  0.540   8.273  21368  Z= 0.315
  Chirality :  0.035   0.138   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.238 178.320   4332
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.51 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.27), residues: 983
  helix:  2.57 (0.21), residues: 628
  sheet:  0.50 (1.02), residues: 24
  loop : -0.95 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.012   0.002   PHE L  50 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.002   0.000   ARG H  79 

Details of bonding type rmsd
  link_TRANS           : bond        0.00032 (    2)
  link_TRANS           : angle       0.23334 (    6)
  hydrogen bonds       : bond        0.05205 (  813)
  hydrogen bonds       : angle       3.03932 ( 2068)
  metal coordination   : bond        0.00543 (    8)
  metal coordination   : angle       4.01284 (    9)
  covalent geometry    : bond        0.00403 (14864)
  covalent geometry    : angle       0.53411 (21353)

*********************** 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
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 1.110 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8436 (pm20)
REVERT: C   73 ASN cc_start: 0.8137 (t0) cc_final: 0.7725 (t0)
REVERT: D   99 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.7945 (mtm-85)
REVERT: H   99 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7750 (mtm180)
REVERT: L    7 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8600 (m110)
REVERT: L   30 MET cc_start: 0.6021 (mmm) cc_final: 0.5633 (mmm)
REVERT: L  147 MET cc_start: 0.6602 (ptp) cc_final: 0.6160 (pmm)
  outliers start: 9
  outliers final: 6
  residues processed: 92
  average time/residue: 0.3785
  time to fit residues: 46.9040
Evaluate side-chains
  93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   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    7 ASN
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    0.0170
   chunk 5 optimal weight:    0.8980
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 116 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
L   7 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 = 0.3558 r_free = 0.3558 target = 0.150140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.111723 restraints weight = 33336.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.77
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1195

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     :  0.524   7.985  21368  Z= 0.307
  Chirality :  0.034   0.134   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.175 178.461   4332
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 10.75 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.27), residues: 983
  helix:  2.64 (0.21), residues: 628
  sheet:  0.53 (1.02), residues: 24
  loop : -0.92 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS H  49 
 PHE   0.011   0.001   PHE L  50 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.004   0.000   ARG L   5 

Details of bonding type rmsd
  link_TRANS           : bond        0.00057 (    2)
  link_TRANS           : angle       0.19317 (    6)
  hydrogen bonds       : bond        0.04797 (  813)
  hydrogen bonds       : angle       2.97200 ( 2068)
  metal coordination   : bond        0.00470 (    8)
  metal coordination   : angle       3.87186 (    9)
  covalent geometry    : bond        0.00320 (14864)
  covalent geometry    : angle       0.51763 (21353)

*********************** 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
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8106 (pm20)
REVERT: D   99 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7581 (mtm-85)
REVERT: H   99 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7331 (mtm180)
REVERT: L   30 MET cc_start: 0.6264 (mmm) cc_final: 0.6004 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 95
  average time/residue: 0.3617
  time to fit residues: 46.3686
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue   37 ILE
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 90 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0980
   chunk 8 optimal weight:    0.0270
   chunk 27 optimal weight:    2.9990
   chunk 117 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.9440

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

Flipped N/Q/H residues before XYZ refinement:
H  47 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 = 0.3551 r_free = 0.3551 target = 0.149443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.111489 restraints weight = 37124.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.89
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1235

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= 0.161
  Angle     :  0.534   8.818  21368  Z= 0.312
  Chirality :  0.035   0.136   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.196 178.388   4332
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.21 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.27), residues: 983
  helix:  2.57 (0.21), residues: 628
  sheet:  0.52 (1.03), residues: 24
  loop : -0.97 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS H  49 
 PHE   0.009   0.001   PHE D  65 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.002   0.000   ARG H  79 

Details of bonding type rmsd
  link_TRANS           : bond        0.00036 (    2)
  link_TRANS           : angle       0.21915 (    6)
  hydrogen bonds       : bond        0.04974 (  813)
  hydrogen bonds       : angle       3.02767 ( 2068)
  metal coordination   : bond        0.00487 (    8)
  metal coordination   : angle       3.96967 (    9)
  covalent geometry    : bond        0.00363 (14864)
  covalent geometry    : angle       0.52780 (21353)

********************** 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
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8118 (pm20)
REVERT: D   99 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7516 (mtm-85)
REVERT: H   99 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.7260 (mtm180)
REVERT: L   30 MET cc_start: 0.6291 (mmm) cc_final: 0.5997 (mmm)
  outliers start: 9
  outliers final: 8
  residues processed: 93
  average time/residue: 0.3570
  time to fit residues: 44.5708
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain L residue   37 ILE
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 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
H  47 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 = 0.3612 r_free = 0.3612 target = 0.151930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.096708 restraints weight = 20789.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.39
r_work: 0.2700 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2684 r_free = 0.2684    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1318

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= 0.180
  Angle     :  0.555   9.064  21368  Z= 0.323
  Chirality :  0.036   0.141   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.347 178.295   4332
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.45 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.27), residues: 983
  helix:  2.49 (0.21), residues: 627
  sheet:  0.52 (1.03), residues: 24
  loop : -1.07 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.011   0.002   PHE D  65 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.002   0.000   ARG H  79 

Details of bonding type rmsd
  link_TRANS           : bond        0.00044 (    2)
  link_TRANS           : angle       0.27053 (    6)
  hydrogen bonds       : bond        0.05492 (  813)
  hydrogen bonds       : angle       3.11399 ( 2068)
  metal coordination   : bond        0.00579 (    8)
  metal coordination   : angle       4.15085 (    9)
  covalent geometry    : bond        0.00415 (14864)
  covalent geometry    : angle       0.54862 (21353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6573.21 seconds
wall clock time: 113 minutes 3.28 seconds (6783.28 seconds total)