Starting phenix.real_space_refine
on Wed Mar  4 11:41:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nzo_0559/03_2026/6nzo_0559.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nzo_0559/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nzo_0559/03_2026/6nzo_0559.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nzo_0559/03_2026/6nzo_0559.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nzo_0559/03_2026/6nzo_0559.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nzo_0559/03_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.99, 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: 1.01
  Conformation dependent library (CDL) restraints added in 367.6 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: 2.10
  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: 2.72

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 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=" 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=" C   ILE G  79 "
       pdb=" N   PRO G  80 "
    ideal  model  delta    sigma   weight residual
    1.334  1.392 -0.058 1.51e-02 4.39e+03 1.45e+01
  bond pdb=" C3'  DC I 143 "
       pdb=" O3'  DC I 143 "
    ideal  model  delta    sigma   weight residual
    1.422  1.500 -0.078 3.00e-02 1.11e+03 6.72e+00
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.495 -0.073 3.00e-02 1.11e+03 5.95e+00
  bond pdb=" C   ILE E  51 "
       pdb=" N   ARG E  52 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.032 1.36e-02 5.41e+03 5.42e+00
  ... (remaining 14566 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 19986
        2.05 -     4.10: 856
        4.10 -     6.15: 49
        6.15 -     8.20: 15
        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=" C   SER S 122 "
        pdb=" N   ASP S 123 "
        pdb=" CA  ASP S 123 "
      ideal   model   delta    sigma   weight residual
     122.61  129.82   -7.21 1.56e+00 4.11e-01 2.14e+01
  angle pdb=" N   VAL S 159 "
        pdb=" CA  VAL S 159 "
        pdb=" C   VAL S 159 "
      ideal   model   delta    sigma   weight residual
     110.05  105.60    4.45 1.09e+00 8.42e-01 1.67e+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: 1700
       0.056 -    0.112: 531
       0.112 -    0.168: 91
       0.168 -    0.224: 23
       0.224 -    0.280: 6
  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=" 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
  chirality pdb=" CA  GLU S 216 "
            pdb=" N   GLU S 216 "
            pdb=" C   GLU S 216 "
            pdb=" CB  GLU S 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+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:             0.900
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.200
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
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      :  0.008   0.165  14583  Z= 0.354
  Angle     :  1.209  47.509  20927  Z= 0.580
  Chirality :  0.056   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
  covalent geometry    : bond        0.00748 (14571)
  covalent geometry    : angle       0.92649 (20909)
  hydrogen bonds       : bond        0.11425 (  811)
  hydrogen bonds       : angle       4.06118 ( 2020)
  metal coordination   : bond        0.07884 (   12)
  metal coordination   : angle      26.49987 (   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  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   54 TYR cc_start: 0.7762 (m-80) cc_final: 0.7551 (m-10)
REVERT: G  102 ILE cc_start: 0.9045 (mt) cc_final: 0.8705 (mm)
REVERT: H   27 ARG cc_start: 0.7646 (mmm160) cc_final: 0.6481 (ptp-170)
REVERT: H   37 TYR cc_start: 0.8260 (m-80) cc_final: 0.8017 (m-80)
REVERT: H   42 LEU cc_start: 0.8182 (tp) cc_final: 0.7826 (tp)
REVERT: H   56 MET cc_start: 0.7287 (tpp) cc_final: 0.7018 (mmp)
REVERT: H   68 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6902 (tm-30)
REVERT: S  201 GLN cc_start: 0.8295 (tt0) cc_final: 0.7894 (tp40)
  outliers start: 1
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1784
  time to fit residues: 60.1138
Evaluate side-chains
  165 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    9.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
B  93 GLN
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  46 HIS
D 106 HIS
E  39 HIS
E  68 GLN
E  85 GLN
F  75 HIS
G  38 ASN
H 106 HIS
** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 215 ASN
S 242 ASN
** S 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 295 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.141901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.115930 restraints weight = 31856.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.118650 restraints weight = 16514.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.120450 restraints weight = 10853.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.121564 restraints weight = 8481.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.122176 restraints weight = 7365.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4058 r_free = 0.4058    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4058 r_free = 0.4058    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14583  Z= 0.154
  Angle     :  0.654  18.344  20927  Z= 0.350
  Chirality :  0.035   0.157   2351
  Planarity :  0.005   0.063   1659
  Dihedral  : 29.957 173.213   4260
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.61 %
    Favored  : 84.82 %
  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:  1.87 (0.21), residues: 559
  sheet: -1.73 (0.80), residues: 45
  loop : -1.44 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  35 
 TYR   0.015   0.002   TYR G  57 
 PHE   0.012   0.001   PHE S 219 
 TRP   0.004   0.001   TRP S 135 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (14571)
  covalent geometry    : angle       0.58237 (20909)
  hydrogen bonds       : bond        0.03905 (  811)
  hydrogen bonds       : angle       3.20596 ( 2020)
  metal coordination   : bond        0.01179 (   12)
  metal coordination   : angle      10.15485 (   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
  235 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 214
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 THR cc_start: 0.8208 (p) cc_final: 0.7821 (t)
REVERT: B   84 MET cc_start: 0.8162 (mmm) cc_final: 0.7319 (ptm)
REVERT: E   63 ARG cc_start: 0.7672 (mmp-170) cc_final: 0.7460 (mmm-85)
REVERT: G   39 TYR cc_start: 0.8338 (m-80) cc_final: 0.8126 (m-80)
REVERT: H   27 ARG cc_start: 0.7728 (mmm160) cc_final: 0.6347 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7798 (tttm) cc_final: 0.7349 (mmtt)
REVERT: H   37 TYR cc_start: 0.8361 (m-80) cc_final: 0.7875 (m-80)
REVERT: H   68 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7304 (tm-30)
REVERT: H   79 HIS cc_start: 0.8069 (t70) cc_final: 0.7719 (t70)
REVERT: H   90 GLU cc_start: 0.7802 (mp0) cc_final: 0.7582 (mp0)
REVERT: S  150 ILE cc_start: 0.9027 (tp) cc_final: 0.8764 (pt)
REVERT: S  154 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8336 (m)
REVERT: S  167 GLU cc_start: 0.7207 (pm20) cc_final: 0.6965 (pm20)
REVERT: S  172 GLN cc_start: 0.6433 (mt0) cc_final: 0.6201 (pt0)
REVERT: S  244 PHE cc_start: 0.5507 (m-80) cc_final: 0.4906 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 225
  average time/residue: 0.1392
  time to fit residues: 43.1029
Evaluate side-chains
  190 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain G residue  107 VAL
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:    0.9980
   chunk 88 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 35 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
G  24 GLN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.140082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.113443 restraints weight = 32267.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.116109 restraints weight = 16797.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.117847 restraints weight = 11151.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.118913 restraints weight = 8794.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.119520 restraints weight = 7695.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4022 r_free = 0.4022    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4022 r_free = 0.4022    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14583  Z= 0.171
  Angle     :  0.629  13.741  20927  Z= 0.348
  Chirality :  0.036   0.159   2351
  Planarity :  0.005   0.057   1659
  Dihedral  : 29.902 173.939   4260
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.06 %
    Favored  : 81.52 %
  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:  1.04 (0.27), residues: 961
  helix:  2.05 (0.21), residues: 559
  sheet: -1.66 (0.79), residues: 45
  loop : -1.25 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  35 
 TYR   0.022   0.002   TYR D  80 
 PHE   0.013   0.002   PHE S 219 
 TRP   0.005   0.001   TRP S 135 
 HIS   0.005   0.001   HIS S 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (14571)
  covalent geometry    : angle       0.58231 (20909)
  hydrogen bonds       : bond        0.04003 (  811)
  hydrogen bonds       : angle       3.13055 ( 2020)
  metal coordination   : bond        0.00876 (   12)
  metal coordination   : angle       8.13132 (   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
  220 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 192
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.7983 (mmm) cc_final: 0.7143 (ptm)
REVERT: C   89 ASN cc_start: 0.8328 (t0) cc_final: 0.8081 (m110)
REVERT: C   92 GLU cc_start: 0.7441 (pm20) cc_final: 0.7141 (pm20)
REVERT: D   68 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: E   63 ARG cc_start: 0.7717 (mmp-170) cc_final: 0.7348 (mmm-85)
REVERT: E  112 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8301 (tp)
REVERT: E  120 MET cc_start: 0.8124 (mtt) cc_final: 0.7850 (mtt)
REVERT: H   27 ARG cc_start: 0.7876 (mmm160) cc_final: 0.6498 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7820 (tttm) cc_final: 0.7398 (mmtt)
REVERT: H   37 TYR cc_start: 0.8418 (m-80) cc_final: 0.7886 (m-80)
REVERT: H   68 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: H   79 HIS cc_start: 0.8064 (t70) cc_final: 0.7717 (t70)
  outliers start: 28
  outliers final: 19
  residues processed: 205
  average time/residue: 0.1196
  time to fit residues: 35.3410
Evaluate side-chains
  201 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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   98 LEU
Chi-restraints excluded: chain D residue  115 VAL
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  112 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  107 VAL
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  218 THR
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:    0.9980
   chunk 93 optimal weight:    6.9990
   chunk 98 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 84 optimal weight:   10.0000
   chunk 119 optimal weight:   20.0000
   chunk 1 optimal weight:    0.7980
   chunk 118 optimal weight:    0.2980
   overall best weight:    2.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
B  27 GLN
** C 104 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 171 ASN
S 242 ASN
** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.138687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.110747 restraints weight = 32225.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.113349 restraints weight = 17197.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.115065 restraints weight = 11621.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.116094 restraints weight = 9260.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.116711 restraints weight = 8154.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3960 r_free = 0.3960    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3960 r_free = 0.3960    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14583  Z= 0.222
  Angle     :  0.670  14.484  20927  Z= 0.370
  Chirality :  0.038   0.165   2351
  Planarity :  0.005   0.056   1659
  Dihedral  : 30.071 173.442   4260
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.63 %
    Favored  : 78.46 %
  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:  1.79 (0.21), residues: 554
  sheet: -1.56 (0.85), residues: 38
  loop : -1.34 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG S 152 
 TYR   0.036   0.002   TYR D  80 
 PHE   0.024   0.002   PHE E  67 
 TRP   0.007   0.002   TRP S 135 
 HIS   0.005   0.001   HIS S 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (14571)
  covalent geometry    : angle       0.63267 (20909)
  hydrogen bonds       : bond        0.04611 (  811)
  hydrogen bonds       : angle       3.33621 ( 2020)
  metal coordination   : bond        0.00861 (   12)
  metal coordination   : angle       7.55676 (   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
  219 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8847 (tp-100) cc_final: 0.7889 (tm-30)
REVERT: C   92 GLU cc_start: 0.7475 (pm20) cc_final: 0.7217 (pm20)
REVERT: D   59 MET cc_start: 0.8333 (tpp) cc_final: 0.8097 (tpp)
REVERT: D   68 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: F  100 PHE cc_start: 0.8071 (m-80) cc_final: 0.7824 (m-10)
REVERT: H   27 ARG cc_start: 0.7901 (mmm160) cc_final: 0.6519 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7875 (tttm) cc_final: 0.7477 (mmtt)
REVERT: H   37 TYR cc_start: 0.8472 (m-80) cc_final: 0.7822 (m-80)
REVERT: H   68 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: S  237 MET cc_start: 0.6369 (ttm) cc_final: 0.6122 (ttm)
  outliers start: 32
  outliers final: 28
  residues processed: 204
  average time/residue: 0.1324
  time to fit residues: 38.2446
Evaluate side-chains
  207 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 179
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   62 ILE
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   38 VAL
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  115 VAL
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 F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  107 VAL
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  150 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 103 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 118 optimal weight:    0.0470
   chunk 25 optimal weight:    5.9990
   chunk 110 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 88 optimal weight:    7.9990
   chunk 111 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   chunk 115 optimal weight:   10.0000
   overall best weight:    1.5682

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

Flipped N/Q/H residues before XYZ refinement:
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  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 172 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 = 0.140248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.112403 restraints weight = 32488.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.115070 restraints weight = 17128.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.116841 restraints weight = 11492.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.117945 restraints weight = 9122.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.118512 restraints weight = 8005.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14583  Z= 0.172
  Angle     :  0.627  13.427  20927  Z= 0.348
  Chirality :  0.036   0.153   2351
  Planarity :  0.005   0.057   1659
  Dihedral  : 30.007 173.376   4260
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 17.63 %
    Favored  : 77.85 %
  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:  0.95 (0.27), residues: 961
  helix:  1.97 (0.22), residues: 553
  sheet: -1.69 (0.83), residues: 38
  loop : -1.24 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 152 
 TYR   0.037   0.002   TYR H  80 
 PHE   0.027   0.002   PHE S 219 
 TRP   0.003   0.001   TRP S 135 
 HIS   0.004   0.001   HIS S 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14571)
  covalent geometry    : angle       0.59148 (20909)
  hydrogen bonds       : bond        0.04020 (  811)
  hydrogen bonds       : angle       3.10726 ( 2020)
  metal coordination   : bond        0.00780 (   12)
  metal coordination   : angle       7.09579 (   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
  223 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 186
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8831 (tp-100) cc_final: 0.7880 (tm-30)
REVERT: B   84 MET cc_start: 0.7884 (mmm) cc_final: 0.7236 (ptm)
REVERT: C   92 GLU cc_start: 0.7505 (pm20) cc_final: 0.7204 (pm20)
REVERT: D   68 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: F   84 MET cc_start: 0.7276 (mmm) cc_final: 0.6945 (mtm)
REVERT: F  100 PHE cc_start: 0.8021 (m-80) cc_final: 0.7761 (m-10)
REVERT: H   27 ARG cc_start: 0.7887 (mmm160) cc_final: 0.6501 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7905 (tttm) cc_final: 0.7528 (mmtt)
REVERT: H   68 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: H   90 GLU cc_start: 0.7754 (mp0) cc_final: 0.7553 (mp0)
REVERT: S  223 MET cc_start: 0.6706 (ptp) cc_final: 0.6398 (ptp)
  outliers start: 37
  outliers final: 26
  residues processed: 207
  average time/residue: 0.1215
  time to fit residues: 35.8547
Evaluate side-chains
  201 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 175
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   80 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 D residue  115 VAL
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 F residue   50 ILE
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain H residue   39 TYR
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  150 ILE
Chi-restraints excluded: chain S residue  172 GLN
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  278 MET
Chi-restraints excluded: chain S residue  287 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 91 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.139177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.111251 restraints weight = 32325.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.113809 restraints weight = 17266.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.115536 restraints weight = 11642.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.116470 restraints weight = 9277.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.117176 restraints weight = 8235.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14583  Z= 0.200
  Angle     :  0.651  13.186  20927  Z= 0.360
  Chirality :  0.037   0.157   2351
  Planarity :  0.005   0.054   1659
  Dihedral  : 30.124 174.969   4260
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 19.71 %
    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:  0.75 (0.27), residues: 961
  helix:  1.75 (0.21), residues: 559
  sheet: -1.51 (0.87), residues: 38
  loop : -1.29 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S 152 
 TYR   0.040   0.002   TYR H  80 
 PHE   0.025   0.002   PHE S 219 
 TRP   0.004   0.001   TRP S 135 
 HIS   0.004   0.001   HIS S 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (14571)
  covalent geometry    : angle       0.61783 (20909)
  hydrogen bonds       : bond        0.04341 (  811)
  hydrogen bonds       : angle       3.21993 ( 2020)
  metal coordination   : bond        0.00738 (   12)
  metal coordination   : angle       7.01558 (   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
  216 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 181
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8837 (tp-100) cc_final: 0.7885 (tm-30)
REVERT: B   58 LEU cc_start: 0.8709 (tp) cc_final: 0.8498 (tp)
REVERT: B   84 MET cc_start: 0.7922 (mmm) cc_final: 0.7221 (ptm)
REVERT: C   92 GLU cc_start: 0.7517 (pm20) cc_final: 0.7235 (pm20)
REVERT: D   68 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7555 (tm-30)
REVERT: F   84 MET cc_start: 0.7043 (mmm) cc_final: 0.6623 (mtm)
REVERT: H   27 ARG cc_start: 0.7918 (mmm160) cc_final: 0.6527 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7762 (tttm) cc_final: 0.7519 (mmtt)
REVERT: H   68 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: H   96 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7872 (ttp80)
  outliers start: 35
  outliers final: 29
  residues processed: 201
  average time/residue: 0.1265
  time to fit residues: 36.1423
Evaluate side-chains
  203 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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   80 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   79 ILE
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   98 LEU
Chi-restraints excluded: chain D residue  115 VAL
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 F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue   39 TYR
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  150 ILE
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  287 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.132232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.103549 restraints weight = 30630.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.106080 restraints weight = 16025.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.107759 restraints weight = 10651.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.108827 restraints weight = 8405.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.109250 restraints weight = 7330.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14583  Z= 0.151
  Angle     :  0.608  12.212  20927  Z= 0.340
  Chirality :  0.035   0.146   2351
  Planarity :  0.004   0.055   1659
  Dihedral  : 30.052 173.483   4260
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.71 %
    Favored  : 76.50 %
  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:  0.94 (0.27), residues: 961
  helix:  1.90 (0.22), residues: 560
  sheet: -1.54 (0.86), residues: 38
  loop : -1.22 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  40 
 TYR   0.034   0.002   TYR H  80 
 PHE   0.024   0.002   PHE S 219 
 TRP   0.002   0.001   TRP S 135 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (14571)
  covalent geometry    : angle       0.58032 (20909)
  hydrogen bonds       : bond        0.03765 (  811)
  hydrogen bonds       : angle       3.03112 ( 2020)
  metal coordination   : bond        0.00748 (   12)
  metal coordination   : angle       6.19126 (   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
  221 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 190
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8802 (tp-100) cc_final: 0.7858 (tm-30)
REVERT: B   84 MET cc_start: 0.7748 (mmm) cc_final: 0.7176 (ptt)
REVERT: C   92 GLU cc_start: 0.7563 (pm20) cc_final: 0.7186 (pm20)
REVERT: D   68 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7499 (tm-30)
REVERT: E   93 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6646 (mt0)
REVERT: F   84 MET cc_start: 0.7089 (mmm) cc_final: 0.6302 (mtm)
REVERT: G   36 LYS cc_start: 0.8343 (tppt) cc_final: 0.8064 (tppt)
REVERT: H   27 ARG cc_start: 0.7846 (mmm160) cc_final: 0.6408 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7900 (tttm) cc_final: 0.7555 (mmtt)
REVERT: H   68 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7560 (tm-30)
REVERT: H   96 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7941 (ttp80)
REVERT: S  233 HIS cc_start: 0.5359 (m-70) cc_final: 0.4995 (t-170)
  outliers start: 31
  outliers final: 24
  residues processed: 206
  average time/residue: 0.1242
  time to fit residues: 36.6225
Evaluate side-chains
  206 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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   80 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   93 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 E residue   90 MET
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   39 TYR
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain S residue  150 ILE
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  287 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 114 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
D  81 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.133079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.103940 restraints weight = 31102.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.106337 restraints weight = 16983.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.107945 restraints weight = 11684.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.108836 restraints weight = 9387.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.109435 restraints weight = 8353.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14583  Z= 0.158
  Angle     :  0.615  13.212  20927  Z= 0.343
  Chirality :  0.035   0.150   2351
  Planarity :  0.004   0.055   1659
  Dihedral  : 30.032 173.732   4260
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.69 %
    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:  0.98 (0.27), residues: 961
  helix:  1.89 (0.22), residues: 559
  sheet: -1.55 (0.85), residues: 38
  loop : -1.10 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F  92 
 TYR   0.032   0.002   TYR H  80 
 PHE   0.024   0.002   PHE S 219 
 TRP   0.002   0.001   TRP S 135 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (14571)
  covalent geometry    : angle       0.59043 (20909)
  hydrogen bonds       : bond        0.03784 (  811)
  hydrogen bonds       : angle       3.03939 ( 2020)
  metal coordination   : bond        0.00727 (   12)
  metal coordination   : angle       5.93815 (   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
  213 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 179
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8834 (tp-100) cc_final: 0.7879 (tm-30)
REVERT: B   84 MET cc_start: 0.7792 (mmm) cc_final: 0.7149 (ptt)
REVERT: C   92 GLU cc_start: 0.7525 (pm20) cc_final: 0.7184 (pm20)
REVERT: D   68 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7477 (tm-30)
REVERT: F   84 MET cc_start: 0.6903 (mmm) cc_final: 0.6391 (mtm)
REVERT: F   92 ARG cc_start: 0.6799 (ttm170) cc_final: 0.6572 (ttm170)
REVERT: H   27 ARG cc_start: 0.7866 (mmm160) cc_final: 0.6416 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7876 (tttm) cc_final: 0.7552 (mmtt)
REVERT: H   48 ASP cc_start: 0.7650 (t0) cc_final: 0.7041 (p0)
REVERT: H   68 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7567 (tm-30)
REVERT: H   96 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8020 (ttp80)
REVERT: S  167 GLU cc_start: 0.7156 (pm20) cc_final: 0.6907 (pm20)
REVERT: S  233 HIS cc_start: 0.5330 (m-70) cc_final: 0.4984 (t-170)
REVERT: S  236 PHE cc_start: 0.6451 (m-80) cc_final: 0.6055 (m-80)
  outliers start: 34
  outliers final: 29
  residues processed: 197
  average time/residue: 0.1238
  time to fit residues: 35.1371
Evaluate side-chains
  209 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 180
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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   80 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   93 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 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   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   39 TYR
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain S residue  150 ILE
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  287 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 75 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 118 optimal weight:   20.0000
   chunk 20 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 92 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.130136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.100647 restraints weight = 31259.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.102991 restraints weight = 17239.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.104501 restraints weight = 11919.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.105347 restraints weight = 9617.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.105953 restraints weight = 8572.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14583  Z= 0.220
  Angle     :  0.674  15.248  20927  Z= 0.371
  Chirality :  0.038   0.157   2351
  Planarity :  0.005   0.052   1659
  Dihedral  : 30.198 178.003   4260
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 20.81 %
    Favored  : 74.54 %
  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:  0.67 (0.27), residues: 961
  helix:  1.60 (0.21), residues: 558
  sheet: -1.65 (0.84), residues: 38
  loop : -1.15 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  92 
 TYR   0.033   0.002   TYR H  80 
 PHE   0.026   0.002   PHE S 219 
 TRP   0.007   0.001   TRP S 135 
 HIS   0.005   0.001   HIS S 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (14571)
  covalent geometry    : angle       0.64444 (20909)
  hydrogen bonds       : bond        0.04500 (  811)
  hydrogen bonds       : angle       3.30473 ( 2020)
  metal coordination   : bond        0.00758 (   12)
  metal coordination   : angle       6.75256 (   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
  217 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 179
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8827 (tp-100) cc_final: 0.7899 (tm-30)
REVERT: C   92 GLU cc_start: 0.7597 (pm20) cc_final: 0.7236 (pm20)
REVERT: D   68 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7595 (tm-30)
REVERT: F   84 MET cc_start: 0.7110 (mmm) cc_final: 0.6794 (tpp)
REVERT: F   92 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6580 (ttm170)
REVERT: H   27 ARG cc_start: 0.7928 (mmm160) cc_final: 0.6492 (ptp-170)
REVERT: H   48 ASP cc_start: 0.7771 (t0) cc_final: 0.7250 (p0)
REVERT: H   68 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: H   90 GLU cc_start: 0.7745 (mp0) cc_final: 0.7083 (mp0)
REVERT: H   96 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7908 (ttp80)
REVERT: S  109 ILE cc_start: 0.4975 (pt) cc_final: 0.4617 (pt)
REVERT: S  167 GLU cc_start: 0.7231 (pm20) cc_final: 0.6965 (pm20)
  outliers start: 38
  outliers final: 33
  residues processed: 201
  average time/residue: 0.1270
  time to fit residues: 36.6593
Evaluate side-chains
  208 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 175
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   93 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 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   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   39 TYR
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  150 ILE
Chi-restraints excluded: chain S residue  179 TYR
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  287 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0050
   chunk 85 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   chunk 102 optimal weight:   20.0000
   overall best weight:    0.9596

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.133022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.104380 restraints weight = 30805.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.106953 restraints weight = 15922.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.108634 restraints weight = 10516.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.109678 restraints weight = 8262.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.110217 restraints weight = 7220.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14583  Z= 0.155
  Angle     :  0.625  14.239  20927  Z= 0.347
  Chirality :  0.036   0.149   2351
  Planarity :  0.004   0.054   1659
  Dihedral  : 30.057 174.328   4260
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.03 %
    Favored  : 74.54 %
  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:  0.91 (0.27), residues: 961
  helix:  1.87 (0.22), residues: 553
  sheet: -1.68 (0.81), residues: 40
  loop : -1.12 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 152 
 TYR   0.033   0.002   TYR D  80 
 PHE   0.025   0.001   PHE S 219 
 TRP   0.002   0.001   TRP S 135 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (14571)
  covalent geometry    : angle       0.59779 (20909)
  hydrogen bonds       : bond        0.03737 (  811)
  hydrogen bonds       : angle       3.07285 ( 2020)
  metal coordination   : bond        0.00704 (   12)
  metal coordination   : angle       6.21442 (   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
  212 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8802 (tp-100) cc_final: 0.7844 (tm-30)
REVERT: B   84 MET cc_start: 0.7940 (mmm) cc_final: 0.7062 (ptt)
REVERT: C   92 GLU cc_start: 0.7599 (pm20) cc_final: 0.7212 (pm20)
REVERT: F   84 MET cc_start: 0.7014 (mmm) cc_final: 0.6668 (tpp)
REVERT: H   27 ARG cc_start: 0.7955 (mmm160) cc_final: 0.6423 (ptp-170)
REVERT: H   28 LYS cc_start: 0.7648 (tttm) cc_final: 0.7374 (mmtt)
REVERT: H   48 ASP cc_start: 0.7706 (t0) cc_final: 0.7203 (p0)
REVERT: H   68 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7514 (tm-30)
REVERT: H   96 ARG cc_start: 0.8402 (tpp80) cc_final: 0.7884 (ttp80)
REVERT: S  167 GLU cc_start: 0.7215 (pm20) cc_final: 0.6950 (pm20)
REVERT: S  233 HIS cc_start: 0.5534 (m-70) cc_final: 0.5116 (t-170)
REVERT: S  244 PHE cc_start: 0.5513 (m-80) cc_final: 0.4630 (m-80)
  outliers start: 28
  outliers final: 27
  residues processed: 200
  average time/residue: 0.1234
  time to fit residues: 35.3237
Evaluate side-chains
  201 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   93 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 E residue   59 GLU
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   39 TYR
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain S residue  150 ILE
Chi-restraints excluded: chain S residue  218 THR
Chi-restraints excluded: chain S residue  272 VAL
Chi-restraints excluded: chain S residue  287 LYS
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:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0170
   chunk 65 optimal weight:    0.6980
   chunk 96 optimal weight:    7.9990
   overall best weight:    1.1422

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.133833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.104818 restraints weight = 30810.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.107256 restraints weight = 16492.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.108854 restraints weight = 11112.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.109750 restraints weight = 8872.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.110330 restraints weight = 7870.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14583  Z= 0.161
  Angle     :  0.633  15.022  20927  Z= 0.349
  Chirality :  0.036   0.150   2351
  Planarity :  0.004   0.055   1659
  Dihedral  : 30.055 174.613   4260
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 21.42 %
    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:  0.93 (0.27), residues: 961
  helix:  1.85 (0.22), residues: 551
  sheet: -1.67 (0.80), residues: 40
  loop : -1.04 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  99 
 TYR   0.026   0.002   TYR H  80 
 PHE   0.025   0.001   PHE E  67 
 TRP   0.002   0.001   TRP S 135 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (14571)
  covalent geometry    : angle       0.60558 (20909)
  hydrogen bonds       : bond        0.03792 (  811)
  hydrogen bonds       : angle       3.08574 ( 2020)
  metal coordination   : bond        0.00714 (   12)
  metal coordination   : angle       6.25539 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2144.98 seconds
wall clock time: 37 minutes 42.61 seconds (2262.61 seconds total)