Starting phenix.real_space_refine
on Thu May 15 22:05:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smw_40604/05_2025/8smw_40604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smw_40604/05_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_40604/05_2025/8smw_40604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smw_40604/05_2025/8smw_40604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smw_40604/05_2025/8smw_40604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smw_40604/05_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.31, per 1000 atoms: 0.67
  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: 3.64
  Conformation dependent library (CDL) restraints added in 1.4 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: 6.65
  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: 5.44

  Time building geometry restraints manager: 4.31 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:             0.850
  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:          0.570
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     42.910
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.060
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.610
-------------------------------------------------------------------------------
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  : 1.171 
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: 0.3956
  time to fit residues: 57.4716
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  : 1.105 
-------------------------------------------------------------------------------
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 = 0.151698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.100800 restraints weight = 20365.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.43
r_work: 0.2724 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2585 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2555 r_free = 0.2555    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 = 0.2555 r_free = 0.2555    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2555
-------------------------------------------------------------------------------
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     :  0.555   7.984  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 : 2.163

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  4.79 %
    Favored  : 94.28 %
  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:  1.90 (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        0.00051 (    2)
  link_TRANS           : angle       0.25182 (    6)
  hydrogen bonds       : bond        0.05429 (  813)
  hydrogen bonds       : angle       3.22183 ( 2068)
  metal coordination   : bond        0.00542 (    8)
  metal coordination   : angle       4.23448 (    9)
  covalent geometry    : bond        0.00400 (14864)
  covalent geometry    : angle       0.54876 (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  : 1.038 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7564 (m-40) cc_final: 0.6913 (t0)
REVERT: D   99 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.7828 (mtm-85)
REVERT: H   46 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8508 (mmtt)
REVERT: H   99 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.7680 (mtm180)
REVERT: L    7 ASN cc_start: 0.8674 (m-40) cc_final: 0.8206 (m110)
REVERT: L   30 MET cc_start: 0.5812 (mmm) cc_final: 0.5525 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 106
  average time/residue: 0.3625
  time to fit residues: 51.3658
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 38 optimal weight:    0.0670
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 101 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 120 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.6918

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.153201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.102703 restraints weight = 21684.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.51
r_work: 0.2826 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    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 = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14874  Z= 0.147
  Angle     :  0.525   7.260  21368  Z= 0.309
  Chirality :  0.034   0.127   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.103 178.443   4332
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.94 %
    Favored  : 91.47 %
  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:  0.50 (1.04), 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   0.002   0.001   HIS H  49 
 PHE   0.010   0.001   PHE L  56 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.003   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00048 (    2)
  link_TRANS           : angle       0.22267 (    6)
  hydrogen bonds       : bond        0.04841 (  813)
  hydrogen bonds       : angle       3.03197 ( 2068)
  metal coordination   : bond        0.00462 (    8)
  metal coordination   : angle       3.98267 (    9)
  covalent geometry    : bond        0.00322 (14864)
  covalent geometry    : angle       0.51909 (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: 5
    poor density    : 96
  time to evaluate  : 1.115 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7416 (m-40) cc_final: 0.6915 (t0)
REVERT: D   99 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.7842 (mtm-85)
REVERT: H   99 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.7732 (mtm180)
REVERT: L   30 MET cc_start: 0.5756 (mmm) cc_final: 0.5433 (mmm)
  outliers start: 5
  outliers final: 4
  residues processed: 99
  average time/residue: 0.3735
  time to fit residues: 49.2451
Evaluate side-chains
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  106 ILE
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:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 120 optimal weight:    5.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.152006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.103217 restraints weight = 27155.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.87
r_work: 0.2681 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    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 = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.0995

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     :  0.530   7.677  21368  Z= 0.311
  Chirality :  0.035   0.133   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.190 178.328   4332
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.18 %
    Favored  : 91.12 %
  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:  2.61 (0.21), residues: 626
  sheet:  0.60 (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   0.009   0.001   PHE D  65 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.002   0.000   ARG L 131 

Details of bonding type rmsd
  link_TRANS           : bond        0.00041 (    2)
  link_TRANS           : angle       0.21743 (    6)
  hydrogen bonds       : bond        0.05029 (  813)
  hydrogen bonds       : angle       3.01696 ( 2068)
  metal coordination   : bond        0.00512 (    8)
  metal coordination   : angle       4.07193 (    9)
  covalent geometry    : bond        0.00355 (14864)
  covalent geometry    : angle       0.52355 (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
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 1.032 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7315 (m-40) cc_final: 0.6885 (t0)
REVERT: D   99 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7776 (mtm-85)
REVERT: H   99 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7590 (mtm180)
REVERT: K   46 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8277 (ttmm)
REVERT: L   30 MET cc_start: 0.5826 (mmm) cc_final: 0.5486 (mmm)
  outliers start: 6
  outliers final: 1
  residues processed: 91
  average time/residue: 0.3633
  time to fit residues: 44.3468
Evaluate side-chains
  88 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   chunk 109 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
L  92 GLN
L 135 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.154098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.099027 restraints weight = 25863.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.80
r_work: 0.2683 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    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 = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1011

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= 0.147
  Angle     :  0.524   7.284  21368  Z= 0.308
  Chirality :  0.034   0.133   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.169 178.454   4332
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.35 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.16 (0.27), residues: 983
  helix:  2.64 (0.21), residues: 626
  sheet:  0.71 (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   0.002   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 L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.17652 (    6)
  hydrogen bonds       : bond        0.04864 (  813)
  hydrogen bonds       : angle       3.01095 ( 2068)
  metal coordination   : bond        0.00477 (    8)
  metal coordination   : angle       3.92664 (    9)
  covalent geometry    : bond        0.00322 (14864)
  covalent geometry    : angle       0.51814 (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
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 1.060 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7217 (m-40) cc_final: 0.7011 (t0)
REVERT: D   99 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.7819 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8598 (mm-30)
REVERT: H   99 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.7620 (mtm180)
REVERT: K   46 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8350 (ttmm)
REVERT: L   30 MET cc_start: 0.5827 (mmm) cc_final: 0.5468 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 89
  average time/residue: 0.3797
  time to fit residues: 44.9277
Evaluate side-chains
  91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 120 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
L  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.148931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.095166 restraints weight = 26101.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.82
r_work: 0.2588 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2565
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2565 r_free = 0.2565    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2565 r_free = 0.2565    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  14874  Z= 0.243
  Angle     :  0.603   8.222  21368  Z= 0.346
  Chirality :  0.039   0.145   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.598 177.844   4332
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.81 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.73 (0.27), residues: 983
  helix:  2.33 (0.21), residues: 625
  sheet:  0.60 (1.02), residues: 24
  loop : -1.20 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K  61 
 HIS   0.004   0.001   HIS H  49 
 PHE   0.013   0.002   PHE D  65 
 TYR   0.011   0.002   TYR H  37 
 ARG   0.004   0.000   ARG F  40 

Details of bonding type rmsd
  link_TRANS           : bond        0.00115 (    2)
  link_TRANS           : angle       0.37854 (    6)
  hydrogen bonds       : bond        0.06582 (  813)
  hydrogen bonds       : angle       3.25769 ( 2068)
  metal coordination   : bond        0.00718 (    8)
  metal coordination   : angle       4.55158 (    9)
  covalent geometry    : bond        0.00579 (14864)
  covalent geometry    : angle       0.59550 (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
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 1.085 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7676 (m-40) cc_final: 0.7097 (t0)
REVERT: D   99 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.7859 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8659 (mm-30)
REVERT: H   99 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.8007 (mtm-85)
REVERT: L   30 MET cc_start: 0.6047 (mmm) cc_final: 0.5651 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 97
  average time/residue: 0.3783
  time to fit residues: 48.9928
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  : 1.151 
-------------------------------------------------------------------------------
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 H residue  119 THR
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 17 optimal weight:    0.1980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 ASN
L  92 GLN
L 135 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.149763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.109150 restraints weight = 27194.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.32
r_work: 0.2603 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14874  Z= 0.149
  Angle     :  0.527   7.338  21368  Z= 0.309
  Chirality :  0.034   0.131   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.179 178.932   4332
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.86 %
    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:  2.05 (0.27), residues: 983
  helix:  2.51 (0.21), residues: 634
  sheet:  0.59 (1.02), residues: 24
  loop : -1.01 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.007   0.000   ARG K  56 

Details of bonding type rmsd
  link_TRANS           : bond        0.00075 (    2)
  link_TRANS           : angle       0.21920 (    6)
  hydrogen bonds       : bond        0.04835 (  813)
  hydrogen bonds       : angle       2.97769 ( 2068)
  metal coordination   : bond        0.00402 (    8)
  metal coordination   : angle       3.99501 (    9)
  covalent geometry    : bond        0.00328 (14864)
  covalent geometry    : angle       0.52031 (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
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 1.176 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7469 (m-40) cc_final: 0.7219 (t0)
REVERT: D   99 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.7928 (mtm-85)
REVERT: D  113 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8772 (mm-30)
REVERT: K   46 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8411 (ttmm)
REVERT: L    7 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8420 (m110)
REVERT: L   30 MET cc_start: 0.6064 (mmm) cc_final: 0.5692 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 99
  average time/residue: 0.3541
  time to fit residues: 47.2863
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue    7 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0010
   chunk 93 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN
L   7 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.151612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.097125 restraints weight = 25984.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 1.81
r_work: 0.2610 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2586 r_free = 0.2586    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 = 0.2586 r_free = 0.2586    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14874  Z= 0.211
  Angle     :  0.577   8.123  21368  Z= 0.333
  Chirality :  0.037   0.144   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.446 178.446   4332
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 10.86 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.80 (0.27), residues: 983
  helix:  2.36 (0.21), residues: 631
  sheet:  0.60 (1.01), residues: 24
  loop : -1.17 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K  61 
 HIS   0.004   0.001   HIS H  49 
 PHE   0.012   0.002   PHE D  65 
 TYR   0.010   0.002   TYR F  51 
 ARG   0.008   0.000   ARG K  56 

Details of bonding type rmsd
  link_TRANS           : bond        0.00048 (    2)
  link_TRANS           : angle       0.32067 (    6)
  hydrogen bonds       : bond        0.05967 (  813)
  hydrogen bonds       : angle       3.18933 ( 2068)
  metal coordination   : bond        0.00646 (    8)
  metal coordination   : angle       4.36766 (    9)
  covalent geometry    : bond        0.00497 (14864)
  covalent geometry    : angle       0.56983 (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
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 1.062 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8352 (pm20)
REVERT: C   73 ASN cc_start: 0.7704 (m-40) cc_final: 0.7262 (t0)
REVERT: D   99 ARG cc_start: 0.8315 (mtt-85) cc_final: 0.7871 (mtm-85)
REVERT: D  113 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8800 (mm-30)
REVERT: K   46 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8315 (ttmm)
REVERT: L    7 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8456 (m110)
REVERT: L   30 MET cc_start: 0.6057 (mmm) cc_final: 0.5668 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 95
  average time/residue: 0.3621
  time to fit residues: 45.9860
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  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   73 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue    7 ASN
Chi-restraints excluded: chain L residue   37 ILE
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:    0.0870
   chunk 5 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.148450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.109571 restraints weight = 33331.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.73
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1276

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= 0.149
  Angle     :  0.539   8.846  21368  Z= 0.315
  Chirality :  0.035   0.135   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.302 178.723   4332
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.45 %
    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:  2.01 (0.27), residues: 983
  helix:  2.53 (0.21), residues: 628
  sheet:  0.64 (1.02), residues: 24
  loop : -1.06 (0.30), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.008   0.000   ARG K  56 

Details of bonding type rmsd
  link_TRANS           : bond        0.00057 (    2)
  link_TRANS           : angle       0.26898 (    6)
  hydrogen bonds       : bond        0.05065 (  813)
  hydrogen bonds       : angle       3.06625 ( 2068)
  metal coordination   : bond        0.00496 (    8)
  metal coordination   : angle       4.04958 (    9)
  covalent geometry    : bond        0.00325 (14864)
  covalent geometry    : angle       0.53274 (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
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 1.155 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8041 (pm20)
REVERT: C   73 ASN cc_start: 0.7507 (m-40) cc_final: 0.7290 (t0)
REVERT: D   99 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7523 (mtm-85)
REVERT: D  113 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8044 (mm-30)
REVERT: K   46 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8584 (ttmm)
REVERT: L   30 MET cc_start: 0.6354 (mmm) cc_final: 0.6085 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 96
  average time/residue: 0.3594
  time to fit residues: 46.5474
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue  100 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0570
   chunk 8 optimal weight:    0.0000
   chunk 27 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6904

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

Flipped N/Q/H residues before XYZ refinement:
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.150607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.112893 restraints weight = 37075.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 2.93
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1267

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     :  0.524   8.793  21368  Z= 0.308
  Chirality :  0.034   0.132   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.105 178.753   4332
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.68 %
    Favored  : 87.27 %
  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:  2.59 (0.21), residues: 629
  sheet:  0.71 (1.02), residues: 24
  loop : -1.03 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  61 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.009   0.001   PHE L  62 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.007   0.000   ARG K  56 

Details of bonding type rmsd
  link_TRANS           : bond        0.00066 (    2)
  link_TRANS           : angle       0.19186 (    6)
  hydrogen bonds       : bond        0.04630 (  813)
  hydrogen bonds       : angle       2.98758 ( 2068)
  metal coordination   : bond        0.00443 (    8)
  metal coordination   : angle       3.87713 (    9)
  covalent geometry    : bond        0.00322 (14864)
  covalent geometry    : angle       0.51831 (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
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 1.041 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8097 (pm20)
REVERT: D   99 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.7548 (mtm-85)
REVERT: L   30 MET cc_start: 0.6331 (mmm) cc_final: 0.6066 (mmm)
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.3554
  time to fit residues: 47.6577
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0000
   chunk 107 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.153131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.100777 restraints weight = 20978.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.50
r_work: 0.2735 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    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 = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1295

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= 0.165
  Angle     :  0.541   9.775  21368  Z= 0.316
  Chirality :  0.035   0.136   2419
  Planarity :  0.004   0.036   1688
  Dihedral  : 29.193 178.562   4332
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.57 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.03 (0.27), residues: 983
  helix:  2.53 (0.21), residues: 628
  sheet:  0.72 (1.03), residues: 24
  loop : -1.03 (0.30), 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   0.009   0.001   PHE D  65 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.007   0.000   ARG K  56 

Details of bonding type rmsd
  link_TRANS           : bond        0.00037 (    2)
  link_TRANS           : angle       0.23325 (    6)
  hydrogen bonds       : bond        0.05036 (  813)
  hydrogen bonds       : angle       3.05838 ( 2068)
  metal coordination   : bond        0.00508 (    8)
  metal coordination   : angle       4.01539 (    9)
  covalent geometry    : bond        0.00372 (14864)
  covalent geometry    : angle       0.53442 (21353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6414.65 seconds
wall clock time: 111 minutes 19.56 seconds (6679.56 seconds total)