Starting phenix.real_space_refine
on Sat Sep 12 03:12:23 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nzo_0559/09_2026/6nzo_0559.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      3      6.06       5
     P     290      5.49       5
     S      32      5.16       5
     C    7707      2.51       5
     N    2563      2.21       5
     O    3143      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13738
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 629
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 797
          Classifications: {'peptide': 104}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 757
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 834
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 4, 'TRANS': 97}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 792
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 752
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2988
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "S"
      Number of atoms: 1816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1816
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "S"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12284  SG  CYS S 143      60.709  80.388  47.265  1.00109.22           S
  ATOM  12396  SG  CYS S 158      59.164  84.192  47.848  1.00101.19           S
  ATOM  12429  SG  CYS S 163      61.766  82.563  50.683  1.00113.64           S
  ATOM  12466  SG  CYS S 169      61.843  82.802  46.265  1.00112.25           S
  ATOM  12173  SG  CYS S 129      58.781  80.486  51.064  1.00112.66           S
  ATOM  12187  SG  CYS S 131      58.804  77.494  49.481  1.00118.61           S
  ATOM  12284  SG  CYS S 143      60.709  80.388  47.265  1.00109.22           S
  ATOM  12325  SG  CYS S 149      58.199  78.606  47.178  1.00 92.28           S
  ATOM  13234  SG  CYS S 261      37.901  89.429  19.020  1.00124.70           S
  ATOM  13613  SG  CYS S 308      40.146  91.851  16.557  1.00133.16           S
  ATOM  13631  SG  CYS S 310      40.500  89.796  15.425  1.00135.88           S
  ATOM  13665  SG  CYS S 315      37.577  90.841  15.137  1.00131.95           S

  Time building chain proxies: 2.96, per 1000 atoms: 0.22
  Number of scatterers: 13738
  At special positions: 0
  Unit cell: (83.2, 146.64, 131.04, 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      3     29.99
     S      32     16.00
     P     290     15.00
     O    3143      8.00
     N    2563      7.00
     C    7707      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
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 408.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN S1001 "
        pdb="ZN    ZN S1001 " - pdb=" SG  CYS S 169 "
        pdb="ZN    ZN S1001 " - pdb=" SG  CYS S 143 "
        pdb="ZN    ZN S1001 " - pdb=" SG  CYS S 158 "
        pdb="ZN    ZN S1001 " - pdb=" SG  CYS S 163 "
      pdb="  ZN S1002 "
        pdb="ZN    ZN S1002 " - pdb=" SG  CYS S 129 "
        pdb="ZN    ZN S1002 " - pdb=" SG  CYS S 149 "
        pdb="ZN    ZN S1002 " - pdb=" SG  CYS S 143 "
        pdb="ZN    ZN S1002 " - pdb=" SG  CYS S 131 "
      pdb="  ZN S1003 "
        pdb="ZN    ZN S1003 " - pdb=" SG  CYS S 308 "
        pdb="ZN    ZN S1003 " - pdb=" SG  CYS S 315 "
        pdb="ZN    ZN S1003 " - pdb=" SG  CYS S 310 "
        pdb="ZN    ZN S1003 " - pdb=" SG  CYS S 261 "
      Number of angles added : 18


  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1832

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 14 sheets defined
      58.8% alpha, 5.8% beta
      143 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.962A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.552A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 3.718A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 17 through 21'
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.561A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.633A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 4.003A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.501A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 77
      removed outlier: 3.926A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.392A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.521A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 120
      removed outlier: 3.546A  pdb=" N   ALA H 104 " --> pdb=" O   PRO H 100 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 151 through 155
      removed outlier: 3.601A  pdb=" N   LYS S 155 " --> pdb=" O   ARG S 152 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 215 through 230
    Processing helix  chain 'S' and resid 252 through 256
      removed outlier: 3.607A  pdb=" N   ARG S 255 " --> pdb=" O   ASN S 252 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE S 256 " --> pdb=" O   LEU S 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 252 through 256'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.828A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.107A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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 100 through 102
      removed outlier: 6.726A  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 35 through 36
    Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.271A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.082A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB3, first strand: chain 'S' and resid 182 through 187
    Processing sheet with id=AB4, first strand: chain 'S' and resid 205 through 208
      removed outlier: 6.715A  pdb=" N   PHE S 205 " --> pdb=" O   ALA S 282 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ALA S 282 " --> pdb=" O   PHE S 205 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 212 through 214

    443 hydrogen bonds defined for protein.
    1284 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 1.51 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: 2233
        1.33 -     1.45: 4991
        1.45 -     1.57: 6723
        1.57 -     1.69: 578
        1.69 -     1.81: 46
  Bond restraints: 14571
  Sorted by residual:
  bond pdb=" C3'  DG J  29 "
       pdb=" O3'  DG J  29 "
    ideal  model  delta    sigma   weight residual
    1.435  1.369  0.066 1.30e-02 5.92e+03 2.56e+01
  bond pdb=" C3'  DC I 143 "
       pdb=" O3'  DC I 143 "
    ideal  model  delta    sigma   weight residual
    1.435  1.500 -0.065 1.30e-02 5.92e+03 2.48e+01
  bond pdb=" C   ASP S 134 "
       pdb=" N   TRP S 135 "
    ideal  model  delta    sigma   weight residual
    1.331  1.390 -0.059 1.23e-02 6.61e+03 2.32e+01
  bond pdb=" C3'  DT J  28 "
       pdb=" O3'  DT J  28 "
    ideal  model  delta    sigma   weight residual
    1.435  1.374  0.061 1.30e-02 5.92e+03 2.17e+01
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.435  1.495 -0.060 1.30e-02 5.92e+03 2.14e+01
  ... (remaining 14566 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 19476
        2.05 -     4.10: 1359
        4.10 -     6.15: 55
        6.15 -     8.20: 16
        8.20 -    10.25: 3
  Bond angle restraints: 20909
  Sorted by residual:
  angle pdb=" N   PRO S  88 "
        pdb=" CA  PRO S  88 "
        pdb=" CB  PRO S  88 "
      ideal   model   delta    sigma   weight residual
     103.00  110.43   -7.43 1.10e+00 8.26e-01 4.56e+01
  angle pdb=" N   PRO S  89 "
        pdb=" CA  PRO S  89 "
        pdb=" CB  PRO S  89 "
      ideal   model   delta    sigma   weight residual
     103.38  110.40   -7.02 1.05e+00 9.07e-01 4.47e+01
  angle pdb=" N   PRO S  84 "
        pdb=" CA  PRO S  84 "
        pdb=" CB  PRO S  84 "
      ideal   model   delta    sigma   weight residual
     103.00  110.24   -7.24 1.10e+00 8.26e-01 4.33e+01
  angle pdb=" O5'  DA J 121 "
        pdb=" C5'  DA J 121 "
        pdb=" C4'  DA J 121 "
      ideal   model   delta    sigma   weight residual
     109.40  113.82   -4.42 8.00e-01 1.56e+00 3.05e+01
  angle pdb=" O4'  DG I 102 "
        pdb=" C1'  DG I 102 "
        pdb=" N9   DG I 102 "
      ideal   model   delta    sigma   weight residual
     108.00  104.26    3.74 7.00e-01 2.04e+00 2.85e+01
  ... (remaining 20904 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.58: 6484
       34.58 -    69.17: 1505
       69.17 -   103.75: 15
      103.75 -   138.33: 0
      138.33 -   172.91: 4
  Dihedral angle restraints: 8008
    sinusoidal: 5161
      harmonic: 2847
  Sorted by residual:
  dihedral pdb=" CA  GLN S 172 "
           pdb=" C   GLN S 172 "
           pdb=" N   ARG S 173 "
           pdb=" CA  ARG S 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.33  -24.67     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  GLU S 133 "
           pdb=" C   GLU S 133 "
           pdb=" N   ASP S 134 "
           pdb=" CA  ASP S 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.48  -24.52     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" C4'  DC J 126 "
           pdb=" C3'  DC J 126 "
           pdb=" O3'  DC J 126 "
           pdb=" P    DC J 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.09  172.91     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 8005 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1588
       0.056 -    0.112: 600
       0.112 -    0.168: 133
       0.168 -    0.224: 23
       0.224 -    0.280: 7
  Chirality restraints: 2351
  Sorted by residual:
  chirality pdb=" CB  ILE H  51 "
            pdb=" CA  ILE H  51 "
            pdb=" CG1 ILE H  51 "
            pdb=" CG2 ILE H  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" C3'  DC J 126 "
            pdb=" C4'  DC J 126 "
            pdb=" O3'  DC J 126 "
            pdb=" C2'  DC J 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.48   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  ILE G 111 "
            pdb=" CA  ILE G 111 "
            pdb=" CG1 ILE G 111 "
            pdb=" CG2 ILE G 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 2348 not shown)

  Planarity restraints: 1659
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 102 "   -0.038 2.00e-02 2.50e+03   1.77e-02 9.39e+00
        pdb=" N9   DG I 102 "    0.032 2.00e-02 2.50e+03
        pdb=" C8   DG I 102 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DG I 102 "    0.023 2.00e-02 2.50e+03
        pdb=" C5   DG I 102 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I 102 "   -0.021 2.00e-02 2.50e+03
        pdb=" O6   DG I 102 "   -0.012 2.00e-02 2.50e+03
        pdb=" N1   DG I 102 "    0.000 2.00e-02 2.50e+03
        pdb=" C2   DG I 102 "    0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I 102 "    0.010 2.00e-02 2.50e+03
        pdb=" N3   DG I 102 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DG I 102 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  20 "   -0.040 2.00e-02 2.50e+03   1.78e-02 8.71e+00
        pdb=" N9   DA I  20 "    0.039 2.00e-02 2.50e+03
        pdb=" C8   DA I  20 "    0.007 2.00e-02 2.50e+03
        pdb=" N7   DA I  20 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  20 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  20 "   -0.012 2.00e-02 2.50e+03
        pdb=" N6   DA I  20 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  20 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  20 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I  20 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DA I  20 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 106 "    0.037 2.00e-02 2.50e+03   1.61e-02 7.82e+00
        pdb=" N9   DG J 106 "   -0.038 2.00e-02 2.50e+03
        pdb=" C8   DG J 106 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG J 106 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DG J 106 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DG J 106 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG J 106 "    0.010 2.00e-02 2.50e+03
        pdb=" N1   DG J 106 "    0.007 2.00e-02 2.50e+03
        pdb=" C2   DG J 106 "   -0.010 2.00e-02 2.50e+03
        pdb=" N2   DG J 106 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG J 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DG J 106 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1656 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3615
        2.83 -     3.35: 11979
        3.35 -     3.87: 27098
        3.87 -     4.38: 30302
        4.38 -     4.90: 43766
  Nonbonded interactions: 116760
  Sorted by model distance:
  nonbonded pdb=" O   CYS S 129 "
            pdb=" ND2 ASN S 164 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   SER D 120 "
            pdb=" OG  SER D 120 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   SER S 260 "
            pdb=" ND2 ASN S 295 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" CB  THR H  29 "
            pdb=" OP1  DT I 104 "
     model   vdw
     2.333 3.470
  nonbonded pdb=" O   LYS S 190 "
            pdb=" ND2 ASN S 258 "
     model   vdw
     2.352 3.120
  ... (remaining 116755 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' and resid 38 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 100)
  selection = (chain 'F' and resid 24 through 100)
}
ncs_group {
  reference = (chain 'C' and resid 16 through 118)
  selection = (chain 'G' and (resid 16 through 35 or (resid 36 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 37 through 118))
}
ncs_group {
  reference = (chain 'D' and resid 26 through 120)
  selection = chain 'H'
}

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=0.89 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.940
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.570
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
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      :  0.009   0.165  14583  Z= 0.764
  Angle     :  1.298  47.509  20927  Z= 0.844
  Chirality :  0.062   0.280   2351
  Planarity :  0.007   0.056   1659
  Dihedral  : 27.022 172.914   6176
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.79 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  5.88 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.24), residues: 961
  helix:  0.15 (0.19), residues: 551
  sheet: -2.07 (0.76), residues: 45
  loop : -1.82 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  92 
 TYR   0.016   0.003   TYR H 118 
 PHE   0.024   0.003   PHE B  61 
 TRP   0.005   0.002   TRP S 135 
 HIS   0.003   0.001   HIS G  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00832 /  0.76 (14571)
  covalent geometry    : angle       1.03950 /  0.83 (20909)
  hydrogen bonds       : bond        0.11425 /  7.53 (  811)
  hydrogen bonds       : angle       4.06118 /  2.95 ( 2020)
  metal coordination   : bond        0.07884 /  4.74 (   12)
  metal coordination   : angle      26.49987 / 15.84 (   18)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 258
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   54 TYR cc_start: 0.7762 (m-80) cc_final: 0.7543 (m-10)
REVERT: G  102 ILE cc_start: 0.9045 (mt) cc_final: 0.8704 (mm)
REVERT: H   27 ARG cc_start: 0.7646 (mmm160) cc_final: 0.6483 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8260 (m-80) cc_final: 0.8027 (m-80)
REVERT: H   42 LEU cc_start: 0.8182 (tp) cc_final: 0.7830 (tp)
REVERT: H   56 MET cc_start: 0.7287 (tpp) cc_final: 0.7034 (mmp)
REVERT: H   68 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6905 (tm-30)
REVERT: S  201 GLN cc_start: 0.8295 (tt0) cc_final: 0.7893 (tp40)
  outliers start: 1
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1741
  time to fit residues: 59.6618
Evaluate side-chains
  166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:   30.0000
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.3182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B  93 GLN
C 104 GLN
D  46 HIS
D 106 HIS
E  39 HIS
E  68 GLN
F  75 HIS
G  38 ASN
H 106 HIS
S 171 ASN
S 215 ASN
S 242 ASN
S 295 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.140328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.113617 restraints weight = 31889.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.116287 restraints weight = 16661.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.118070 restraints weight = 11086.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.119055 restraints weight = 8715.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.119749 restraints weight = 7668.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.4025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14583  Z= 0.157
  Angle     :  0.824  27.128  20927  Z= 0.410
  Chirality :  0.051   0.346   2351
  Planarity :  0.005   0.060   1659
  Dihedral  : 30.621 176.695   4260
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.48 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.27), residues: 961
  helix:  1.52 (0.21), residues: 558
  sheet: -1.72 (0.82), residues: 44
  loop : -1.52 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  35 
 TYR   0.019   0.002   TYR G  39 
 PHE   0.014   0.002   PHE S 219 
 TRP   0.005   0.001   TRP S 135 
 HIS   0.010   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.16 (14571)
  covalent geometry    : angle       0.71436 /  0.40 (20909)
  hydrogen bonds       : bond        0.05221 /  3.45 (  811)
  hydrogen bonds       : angle       3.50815 /  2.58 ( 2020)
  metal coordination   : bond        0.01622 /  0.94 (   12)
  metal coordination   : angle      14.05053 /  9.69 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8468 (ttmt)
REVERT: B   40 ARG cc_start: 0.8728 (ttm170) cc_final: 0.8423 (ttm170)
REVERT: G   39 TYR cc_start: 0.8428 (m-80) cc_final: 0.8132 (m-80)
REVERT: G  102 ILE cc_start: 0.9193 (mt) cc_final: 0.8968 (mm)
REVERT: G  104 GLN cc_start: 0.8569 (mp10) cc_final: 0.8162 (mp10)
REVERT: H   27 ARG cc_start: 0.7740 (mmm160) cc_final: 0.6301 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8467 (m-80) cc_final: 0.7869 (m-80)
REVERT: H   68 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7278 (tm-30)
REVERT: H   79 HIS cc_start: 0.8144 (t70) cc_final: 0.7923 (t70)
REVERT: S  154 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8404 (m)
REVERT: S  185 ILE cc_start: 0.6159 (tp) cc_final: 0.5889 (tp)
REVERT: S  227 ASP cc_start: 0.6554 (m-30) cc_final: 0.6103 (p0)
REVERT: S  244 PHE cc_start: 0.5545 (m-80) cc_final: 0.4872 (m-80)
  outliers start: 24
  outliers final: 15
  residues processed: 214
  average time/residue: 0.1358
  time to fit residues: 41.0182
Evaluate side-chains
  194 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 178
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  154 THR
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  272 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 88 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 84 optimal weight:   40.0000
   chunk 22 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0070
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
G  24 GLN
S 170 GLN
S 172 GLN
S 242 ASN
** S 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.141693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.115304 restraints weight = 32233.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.118019 restraints weight = 16625.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.119833 restraints weight = 10960.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.120875 restraints weight = 8574.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.121515 restraints weight = 7497.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (8 function evaluations)
r_final: 0.4049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  14583  Z= 0.137
  Angle     :  0.711  21.425  20927  Z= 0.375
  Chirality :  0.047   0.330   2351
  Planarity :  0.005   0.061   1659
  Dihedral  : 30.424 176.438   4260
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.08 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.27), residues: 961
  helix:  1.92 (0.21), residues: 560
  sheet: -1.63 (0.81), residues: 40
  loop : -1.45 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  35 
 TYR   0.018   0.002   TYR A  41 
 PHE   0.016   0.001   PHE S 236 
 TRP   0.001   0.001   TRP S 270 
 HIS   0.008   0.001   HIS S 141 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.14 (14571)
  covalent geometry    : angle       0.64524 /  0.37 (20909)
  hydrogen bonds       : bond        0.04575 /  3.01 (  811)
  hydrogen bonds       : angle       3.25392 /  2.40 ( 2020)
  metal coordination   : bond        0.01166 /  0.63 (   12)
  metal coordination   : angle      10.22504 /  7.10 (   18)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8409 (ttpp) cc_final: 0.8126 (ttmt)
REVERT: A   68 GLN cc_start: 0.8679 (tp-100) cc_final: 0.7937 (tm-30)
REVERT: B   74 GLU cc_start: 0.7868 (tt0) cc_final: 0.7613 (tt0)
REVERT: C   84 GLN cc_start: 0.8038 (tp40) cc_final: 0.7815 (tp40)
REVERT: C   92 GLU cc_start: 0.7356 (pm20) cc_final: 0.7108 (pm20)
REVERT: G  104 GLN cc_start: 0.8402 (mp10) cc_final: 0.8155 (mp10)
REVERT: H   27 ARG cc_start: 0.7783 (mmm160) cc_final: 0.6383 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8498 (m-80) cc_final: 0.7977 (m-80)
REVERT: H   68 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7281 (tm-30)
REVERT: H   79 HIS cc_start: 0.8086 (t70) cc_final: 0.7745 (t70)
REVERT: H   85 THR cc_start: 0.8975 (m) cc_final: 0.8575 (p)
REVERT: S  141 HIS cc_start: 0.5348 (m-70) cc_final: 0.4930 (m170)
REVERT: S  154 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8321 (m)
REVERT: S  227 ASP cc_start: 0.6467 (m-30) cc_final: 0.6248 (p0)
REVERT: S  278 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7638 (mtm)
  outliers start: 27
  outliers final: 15
  residues processed: 215
  average time/residue: 0.1330
  time to fit residues: 40.7153
Evaluate side-chains
  195 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  154 THR
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  253 LEU
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  278 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 98 optimal weight:   30.0000
   chunk 88 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 75 optimal weight:   20.0000
   chunk 84 optimal weight:   30.0000
   chunk 119 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 118 optimal weight:    9.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 242 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.136201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.108485 restraints weight = 31904.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.110954 restraints weight = 17152.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.112624 restraints weight = 11582.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.113540 restraints weight = 9209.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.114192 restraints weight = 8150.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3941 r_free = 0.3941    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3941 r_free = 0.3941    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.3941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  14583  Z= 0.255
  Angle     :  0.820  18.605  20927  Z= 0.426
  Chirality :  0.051   0.341   2351
  Planarity :  0.006   0.059   1659
  Dihedral  : 30.590 176.345   4260
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 15.67 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.27), residues: 961
  helix:  1.52 (0.21), residues: 559
  sheet: -1.69 (0.83), residues: 40
  loop : -1.45 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 116 
 TYR   0.027   0.002   TYR D  80 
 PHE   0.024   0.002   PHE E  67 
 TRP   0.006   0.002   TRP S 135 
 HIS   0.007   0.002   HIS G  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00531 /  0.26 (14571)
  covalent geometry    : angle       0.76697 /  0.42 (20909)
  hydrogen bonds       : bond        0.05746 /  3.82 (  811)
  hydrogen bonds       : angle       3.58833 /  2.64 ( 2020)
  metal coordination   : bond        0.01054 /  0.64 (   12)
  metal coordination   : angle       9.93467 /  7.28 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 183
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8439 (ttmt)
REVERT: B   84 MET cc_start: 0.8026 (mmm) cc_final: 0.7208 (ptm)
REVERT: C   92 GLU cc_start: 0.7469 (pm20) cc_final: 0.7209 (pm20)
REVERT: D   68 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7533 (tm-30)
REVERT: G  104 GLN cc_start: 0.8554 (mp10) cc_final: 0.8240 (mp10)
REVERT: H   27 ARG cc_start: 0.7799 (mmm160) cc_final: 0.6516 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8580 (m-80) cc_final: 0.8058 (m-80)
REVERT: H   68 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: S  214 ILE cc_start: 0.5051 (OUTLIER) cc_final: 0.4708 (pt)
REVERT: S  223 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7394 (ptp)
REVERT: S  227 ASP cc_start: 0.6474 (m-30) cc_final: 0.6253 (p0)
REVERT: S  278 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7457 (mtm)
  outliers start: 42
  outliers final: 33
  residues processed: 205
  average time/residue: 0.1228
  time to fit residues: 36.7059
Evaluate side-chains
  207 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 171
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   89 ASN
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain S residue  185 ILE
Chi-restraints excluded: chain S residue  214 ILE
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  253 LEU
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  259 HIS
Chi-restraints excluded: chain S residue  265 CYS
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  278 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 110 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 88 optimal weight:   20.0000
   chunk 111 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 115 optimal weight:    9.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 172 GLN
S 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.137840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.109436 restraints weight = 32312.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.112113 restraints weight = 17149.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.113856 restraints weight = 11532.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.114921 restraints weight = 9151.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.115429 restraints weight = 8053.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14583  Z= 0.203
  Angle     :  0.757  17.166  20927  Z= 0.400
  Chirality :  0.049   0.342   2351
  Planarity :  0.005   0.060   1659
  Dihedral  : 30.624 176.234   4260
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 18.48 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.27), residues: 961
  helix:  1.57 (0.21), residues: 559
  sheet: -1.08 (0.94), residues: 30
  loop : -1.55 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  35 
 TYR   0.036   0.002   TYR D  80 
 PHE   0.020   0.002   PHE B 100 
 TRP   0.005   0.001   TRP S 135 
 HIS   0.004   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.20 (14571)
  covalent geometry    : angle       0.70781 /  0.40 (20909)
  hydrogen bonds       : bond        0.05144 /  3.43 (  811)
  hydrogen bonds       : angle       3.46756 /  2.55 ( 2020)
  metal coordination   : bond        0.00923 /  0.56 (   12)
  metal coordination   : angle       9.17530 /  6.55 (   18)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8453 (ttmt)
REVERT: A   68 GLN cc_start: 0.8841 (tp-100) cc_final: 0.7894 (tm-30)
REVERT: B   84 MET cc_start: 0.8053 (mmm) cc_final: 0.7264 (ptm)
REVERT: C   92 GLU cc_start: 0.7486 (pm20) cc_final: 0.7168 (pm20)
REVERT: D   68 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7584 (tm-30)
REVERT: G  104 GLN cc_start: 0.8576 (mp10) cc_final: 0.8222 (mp10)
REVERT: H   27 ARG cc_start: 0.7929 (mmm160) cc_final: 0.6521 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8541 (m-80) cc_final: 0.7996 (m-80)
REVERT: H   68 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: S  214 ILE cc_start: 0.4862 (OUTLIER) cc_final: 0.4631 (pt)
REVERT: S  223 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7517 (ptp)
  outliers start: 35
  outliers final: 26
  residues processed: 201
  average time/residue: 0.1237
  time to fit residues: 35.9488
Evaluate side-chains
  205 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  185 ILE
Chi-restraints excluded: chain S residue  214 ILE
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  272 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 91 optimal weight:   30.0000
   chunk 66 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 107 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 81 optimal weight:   30.0000
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 172 GLN
S 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.140763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.113196 restraints weight = 32153.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.115940 restraints weight = 16660.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.117753 restraints weight = 11078.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.118812 restraints weight = 8745.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.119471 restraints weight = 7687.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14583  Z= 0.138
  Angle     :  0.684  16.315  20927  Z= 0.369
  Chirality :  0.046   0.325   2351
  Planarity :  0.005   0.059   1659
  Dihedral  : 30.509 177.128   4260
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.93 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.27), residues: 961
  helix:  1.82 (0.21), residues: 559
  sheet: -1.47 (0.87), residues: 40
  loop : -1.38 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  35 
 TYR   0.040   0.002   TYR D  80 
 PHE   0.034   0.002   PHE E  67 
 TRP   0.003   0.001   TRP S 135 
 HIS   0.005   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.14 (14571)
  covalent geometry    : angle       0.64037 /  0.37 (20909)
  hydrogen bonds       : bond        0.04522 /  3.01 (  811)
  hydrogen bonds       : angle       3.23803 /  2.38 ( 2020)
  metal coordination   : bond        0.00825 /  0.46 (   12)
  metal coordination   : angle       8.24332 /  5.86 (   18)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 196
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7824 (p0)
REVERT: C   92 GLU cc_start: 0.7444 (pm20) cc_final: 0.7110 (pm20)
REVERT: D   68 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: G  104 GLN cc_start: 0.8565 (mp10) cc_final: 0.8219 (mp10)
REVERT: H   27 ARG cc_start: 0.7899 (mmm160) cc_final: 0.6501 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8524 (m-80) cc_final: 0.7898 (m-80)
REVERT: H   68 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7400 (tm-30)
REVERT: H   79 HIS cc_start: 0.8064 (t70) cc_final: 0.7741 (t70)
REVERT: H   96 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7914 (ttp80)
REVERT: S  223 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7725 (ptp)
  outliers start: 25
  outliers final: 15
  residues processed: 208
  average time/residue: 0.1289
  time to fit residues: 38.4945
Evaluate side-chains
  204 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  185 ILE
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  272 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 46 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 83 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 89 optimal weight:   30.0000
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
D  81 ASN
S 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.139674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.112906 restraints weight = 31693.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.115572 restraints weight = 16502.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.117297 restraints weight = 10987.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.118233 restraints weight = 8705.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.118891 restraints weight = 7714.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14583  Z= 0.139
  Angle     :  0.692  16.608  20927  Z= 0.370
  Chirality :  0.046   0.389   2351
  Planarity :  0.005   0.058   1659
  Dihedral  : 30.471 177.507   4260
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 21.66 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.27), residues: 961
  helix:  1.85 (0.22), residues: 555
  sheet: -1.33 (0.92), residues: 35
  loop : -1.32 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  30 
 TYR   0.040   0.002   TYR H  80 
 PHE   0.027   0.002   PHE E  67 
 TRP   0.003   0.001   TRP S 135 
 HIS   0.004   0.001   HIS S 259 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.14 (14571)
  covalent geometry    : angle       0.65117 /  0.37 (20909)
  hydrogen bonds       : bond        0.04419 /  2.94 (  811)
  hydrogen bonds       : angle       3.23209 /  2.36 ( 2020)
  metal coordination   : bond        0.00842 /  0.47 (   12)
  metal coordination   : angle       8.03626 /  5.75 (   18)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.7446 (pm20) cc_final: 0.7083 (pm20)
REVERT: D   68 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: F   98 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6973 (m-10)
REVERT: G  104 GLN cc_start: 0.8569 (mp10) cc_final: 0.8145 (mp10)
REVERT: H   27 ARG cc_start: 0.7857 (mmm160) cc_final: 0.6504 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8554 (m-80) cc_final: 0.7945 (m-80)
REVERT: H   68 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7436 (tm-30)
REVERT: H   79 HIS cc_start: 0.8089 (t70) cc_final: 0.7736 (t70)
REVERT: H   96 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7939 (ttp80)
REVERT: S  223 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7702 (ptp)
  outliers start: 24
  outliers final: 17
  residues processed: 202
  average time/residue: 0.1263
  time to fit residues: 36.8496
Evaluate side-chains
  199 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  185 ILE
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  272 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 77 optimal weight:   20.0000
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 242 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.140905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.113435 restraints weight = 32017.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.116166 restraints weight = 16567.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.117983 restraints weight = 11030.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.119080 restraints weight = 8729.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.119643 restraints weight = 7652.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14583  Z= 0.142
  Angle     :  0.688  16.654  20927  Z= 0.369
  Chirality :  0.045   0.334   2351
  Planarity :  0.005   0.058   1659
  Dihedral  : 30.454 177.884   4260
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 21.54 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.28), residues: 961
  helix:  1.86 (0.22), residues: 555
  sheet: -1.42 (0.86), residues: 40
  loop : -1.25 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  30 
 TYR   0.046   0.002   TYR H  80 
 PHE   0.014   0.001   PHE S 219 
 TRP   0.003   0.001   TRP S 135 
 HIS   0.004   0.001   HIS S 259 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.14 (14571)
  covalent geometry    : angle       0.64965 /  0.37 (20909)
  hydrogen bonds       : bond        0.04388 /  2.92 (  811)
  hydrogen bonds       : angle       3.25386 /  2.38 ( 2020)
  metal coordination   : bond        0.00769 /  0.43 (   12)
  metal coordination   : angle       7.77104 /  5.46 (   18)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8842 (tp-100) cc_final: 0.7823 (tm-30)
REVERT: C   92 GLU cc_start: 0.7432 (pm20) cc_final: 0.7082 (pm20)
REVERT: D   68 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: F   98 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6737 (m-10)
REVERT: G  104 GLN cc_start: 0.8605 (mp10) cc_final: 0.8158 (mp10)
REVERT: H   27 ARG cc_start: 0.7840 (mmm160) cc_final: 0.6494 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8529 (m-80) cc_final: 0.7899 (m-80)
REVERT: H   68 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7434 (tm-30)
REVERT: H   79 HIS cc_start: 0.8073 (t70) cc_final: 0.7811 (t70)
REVERT: H   96 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7905 (ttp80)
REVERT: S  223 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7714 (ptp)
  outliers start: 25
  outliers final: 20
  residues processed: 196
  average time/residue: 0.1282
  time to fit residues: 36.2968
Evaluate side-chains
  198 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  185 ILE
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  272 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 75 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9990
   chunk 118 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 78 optimal weight:   30.0000
   chunk 67 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 97 optimal weight:   30.0000
   chunk 92 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 242 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.140250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.112555 restraints weight = 32290.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.115276 restraints weight = 16797.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.117047 restraints weight = 11205.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.118148 restraints weight = 8873.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.118684 restraints weight = 7804.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14583  Z= 0.159
  Angle     :  0.701  13.652  20927  Z= 0.377
  Chirality :  0.046   0.336   2351
  Planarity :  0.005   0.059   1659
  Dihedral  : 30.483 177.976   4260
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.66 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.27), residues: 961
  helix:  1.75 (0.21), residues: 555
  sheet: -1.54 (0.87), residues: 40
  loop : -1.29 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  30 
 TYR   0.044   0.002   TYR H  80 
 PHE   0.025   0.002   PHE E  67 
 TRP   0.002   0.001   TRP S 135 
 HIS   0.007   0.001   HIS S 141 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 (14571)
  covalent geometry    : angle       0.66769 /  0.38 (20909)
  hydrogen bonds       : bond        0.04492 /  2.99 (  811)
  hydrogen bonds       : angle       3.28652 /  2.40 ( 2020)
  metal coordination   : bond        0.00738 /  0.43 (   12)
  metal coordination   : angle       7.35380 /  5.31 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8857 (tp-100) cc_final: 0.7832 (tm-30)
REVERT: C   92 GLU cc_start: 0.7441 (pm20) cc_final: 0.7079 (pm20)
REVERT: D   68 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: F   98 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6899 (m-10)
REVERT: G  104 GLN cc_start: 0.8596 (mp10) cc_final: 0.8161 (mp10)
REVERT: H   27 ARG cc_start: 0.7890 (mmm160) cc_final: 0.6495 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8559 (m-80) cc_final: 0.7914 (m-80)
REVERT: H   68 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: H   79 HIS cc_start: 0.8046 (t70) cc_final: 0.7818 (t70)
REVERT: H   96 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8161 (ttp80)
REVERT: S  223 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7705 (ptp)
  outliers start: 29
  outliers final: 24
  residues processed: 200
  average time/residue: 0.1258
  time to fit residues: 36.2388
Evaluate side-chains
  206 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  185 ILE
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  256 PHE
Chi-restraints excluded: chain S residue  265 CYS
Chi-restraints excluded: chain S residue  272 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 101 optimal weight:    9.9990
   chunk 85 optimal weight:   50.0000
   chunk 12 optimal weight:    0.7980
   chunk 86 optimal weight:   30.0000
   chunk 6 optimal weight:    0.9980
   chunk 103 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 74 optimal weight:   20.0000
   chunk 102 optimal weight:   10.0000
   overall best weight:    1.4582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 242 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.140760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.113179 restraints weight = 32222.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.115910 restraints weight = 16654.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.117699 restraints weight = 11082.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.118767 restraints weight = 8777.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.119395 restraints weight = 7709.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14583  Z= 0.151
  Angle     :  0.691  13.993  20927  Z= 0.373
  Chirality :  0.045   0.343   2351
  Planarity :  0.005   0.072   1659
  Dihedral  : 30.478 178.298   4260
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 22.77 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.27), residues: 961
  helix:  1.74 (0.21), residues: 555
  sheet: -1.55 (0.86), residues: 40
  loop : -1.24 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F  95 
 TYR   0.046   0.002   TYR H  80 
 PHE   0.012   0.001   PHE B  61 
 TRP   0.003   0.001   TRP S 135 
 HIS   0.005   0.001   HIS S 141 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.15 (14571)
  covalent geometry    : angle       0.65920 /  0.37 (20909)
  hydrogen bonds       : bond        0.04402 /  2.93 (  811)
  hydrogen bonds       : angle       3.25802 /  2.38 ( 2020)
  metal coordination   : bond        0.00741 /  0.42 (   12)
  metal coordination   : angle       7.14826 /  5.08 (   18)

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

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

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1922 Ramachandran restraints generated.
    961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 181
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8845 (tp-100) cc_final: 0.7863 (tm-30)
REVERT: C   92 GLU cc_start: 0.7476 (pm20) cc_final: 0.7093 (pm20)
REVERT: D   68 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7405 (tm-30)
REVERT: F   84 MET cc_start: 0.7257 (mmp) cc_final: 0.6727 (mtp)
REVERT: F   92 ARG cc_start: 0.6499 (ttt180) cc_final: 0.6131 (ttt180)
REVERT: F   98 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6942 (m-10)
REVERT: G  104 GLN cc_start: 0.8605 (mp10) cc_final: 0.8121 (mp10)
REVERT: H   27 ARG cc_start: 0.7889 (mmm160) cc_final: 0.6515 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8571 (m-80) cc_final: 0.7905 (m-80)
REVERT: H   68 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: H   79 HIS cc_start: 0.8050 (t70) cc_final: 0.7738 (t70)
REVERT: S  223 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7679 (ptp)
  outliers start: 23
  outliers final: 19
  residues processed: 192
  average time/residue: 0.1234
  time to fit residues: 34.6068
Evaluate side-chains
  195 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   98 TYR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain S residue  185 ILE
Chi-restraints excluded: chain S residue  223 MET
Chi-restraints excluded: chain S residue  272 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 77 optimal weight:   20.0000
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0970
   chunk 65 optimal weight:    0.7980
   chunk 96 optimal weight:   20.0000
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 242 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.142773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.115456 restraints weight = 32566.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.118268 restraints weight = 16706.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.120107 restraints weight = 11007.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.121225 restraints weight = 8665.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.121825 restraints weight = 7579.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14583  Z= 0.135
  Angle     :  0.671  17.081  20927  Z= 0.363
  Chirality :  0.044   0.357   2351
  Planarity :  0.005   0.068   1659
  Dihedral  : 30.420 178.868   4260
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.40 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.27), residues: 961
  helix:  1.86 (0.22), residues: 555
  sheet: -1.52 (0.84), residues: 40
  loop : -1.17 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  95 
 TYR   0.041   0.002   TYR H  80 
 PHE   0.016   0.002   PHE E  67 
 TRP   0.004   0.001   TRP S 135 
 HIS   0.006   0.001   HIS S 141 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.13 (14571)
  covalent geometry    : angle       0.63620 /  0.36 (20909)
  hydrogen bonds       : bond        0.04162 /  2.77 (  811)
  hydrogen bonds       : angle       3.14371 /  2.30 ( 2020)
  metal coordination   : bond        0.01005 /  0.50 (   12)
  metal coordination   : angle       7.34887 /  5.08 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2258.61 seconds
wall clock time: 39 minutes 44.52 seconds (2384.52 seconds total)