Starting phenix.real_space_refine
on Sat Jul  4 19:10:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v9x_64891/07_2026/9v9x_64891.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v9x_64891/07_2026/9v9x_64891.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v9x_64891/07_2026/9v9x_64891.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v9x_64891/07_2026/9v9x_64891.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v9x_64891/07_2026/9v9x_64891.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v9x_64891/07_2026/9v9x_64891.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 12492 atoms to isotropic.
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      4      6.06       5
     P     261      5.49       5
     S      31      5.16       5
     C    7329      2.51       5
     N    2413      2.21       5
     O    2929      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12967
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 774
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 714
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "E"
      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: "F"
      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: "G"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 708
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 2650
          Classifications: {'DNA': 130}
          Link IDs: {'rna3p': 129}
    Chain: "J"
      Number of atoms: 2701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2701
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
    Chain: "M"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 967
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "N"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 793
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 7, 'TRANS': 92}
    Chain: "M"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "N"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  11324  SG  CYS M  18      68.322  27.302  74.368  1.00 87.86           S
  ATOM  11345  SG  CYS M  21      66.501  23.691  74.782  1.00 91.25           S
  ATOM  11483  SG  CYS M  39      67.371  25.331  71.398  1.00 84.00           S
  ATOM  11505  SG  CYS M  42      64.635  26.612  73.703  1.00 79.81           S
  ATOM  11442  SG  CYS M  34      72.170  40.310  73.263  1.00 70.21           S
  ATOM  11600  SG  CYS M  53      69.547  39.027  75.864  1.00 75.91           S
  ATOM  11621  SG  CYS M  56      72.035  41.765  76.776  1.00 77.53           S
  ATOM  12459  SG  CYS N  51      86.666  40.305  55.283  1.00 82.41           S
  ATOM  12480  SG  CYS N  54      90.368  39.650  55.452  1.00 85.68           S
  ATOM  12628  SG  CYS N  72      88.333  40.299  58.665  1.00 76.71           S
  ATOM  12647  SG  CYS N  75      89.159  43.116  56.273  1.00 73.13           S
  ATOM  12582  SG  CYS N  67      73.604  41.275  55.667  1.00 66.35           S
  ATOM  12736  SG  CYS N  87      76.232  42.863  53.330  1.00 72.14           S
  ATOM  12756  SG  CYS N  90      72.500  43.016  52.483  1.00 72.57           S

  Time building chain proxies: 2.77, per 1000 atoms: 0.21
  Number of scatterers: 12967
  At special positions: 0
  Unit cell: (124.3, 121, 118.8, 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      4     29.99
     S      31     16.00
     P     261     15.00
     O    2929      8.00
     N    2413      7.00
     C    7329      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: 0.99
  Conformation dependent library (CDL) restraints added in 401.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN M 401 "
        pdb="ZN    ZN M 401 " - pdb=" SG  CYS M  42 "
        pdb="ZN    ZN M 401 " - pdb=" SG  CYS M  39 "
        pdb="ZN    ZN M 401 " - pdb=" SG  CYS M  21 "
        pdb="ZN    ZN M 401 " - pdb=" SG  CYS M  18 "
      pdb="  ZN M 402 "
        pdb="ZN    ZN M 402 " - pdb=" ND1 HIS M  36 "
        pdb="ZN    ZN M 402 " - pdb=" SG  CYS M  56 "
        pdb="ZN    ZN M 402 " - pdb=" SG  CYS M  34 "
        pdb="ZN    ZN M 402 " - pdb=" SG  CYS M  53 "
      pdb="  ZN N 401 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  54 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  51 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  72 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  75 "
      pdb="  ZN N 402 "
        pdb="ZN    ZN N 402 " - pdb=" ND1 HIS N  69 "
        pdb="ZN    ZN N 402 " - pdb=" SG  CYS N  67 "
        pdb="ZN    ZN N 402 " - pdb=" SG  CYS N  90 "
        pdb="ZN    ZN N 402 " - pdb=" SG  CYS N  87 "
      Number of angles added : 18


  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 12 sheets defined
      65.2% alpha, 3.8% beta
      125 base pairs and 211 stacking pairs defined.
    Time for finding SS restraints: 1.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.982A  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 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.996A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.638A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.435A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.682A  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 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.544A  pdb=" N   MET D  56 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 119
      removed outlier: 3.878A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.644A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.891A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.524A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 16 through 21'
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.411A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (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
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 4.041A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 8 through 13
    Processing helix  chain 'M' and resid 14 through 16
      No H-bonds generated for 'chain 'M' and resid 14 through 16'
    Processing helix  chain 'M' and resid 39 through 48
      removed outlier: 3.629A  pdb=" N   GLU M  48 " --> pdb=" O   VAL M  44 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 64 through 67
    Processing helix  chain 'M' and resid 72 through 83
    Processing helix  chain 'M' and resid 85 through 98
    Processing helix  chain 'M' and resid 110 through 115
      removed outlier: 3.635A  pdb=" N   ARG M 114 " --> pdb=" O   SER M 110 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 20 through 25
      removed outlier: 4.381A  pdb=" N   GLN N  25 " --> pdb=" O   LEU N  21 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 73 through 83
    Processing helix  chain 'N' and resid 96 through 98
      No H-bonds generated for 'chain 'N' and resid 96 through 98'
    Processing helix  chain 'N' and resid 103 through 114
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.804A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.652A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.207A  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
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.110A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.377A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'M' and resid 37 through 38
    Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 72

    444 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      321 hydrogen bonds
      638 hydrogen bond angles
      0 basepair planarities
      125 basepair parallelities
      211 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3127
        1.34 -     1.46: 3777
        1.46 -     1.58: 6253
        1.58 -     1.69: 520
        1.69 -     1.81: 46
  Bond restraints: 13723
  Sorted by residual:
  bond pdb=" C3'  DT J  88 "
       pdb=" C2'  DT J  88 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.18e+01
  bond pdb=" C3'  DT J  57 "
       pdb=" C2'  DT J  57 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.14e+01
  bond pdb=" C3'  DT I 104 "
       pdb=" C2'  DT I 104 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.08e+01
  bond pdb=" C3'  DC J  77 "
       pdb=" C2'  DC J  77 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.07e+01
  bond pdb=" C3'  DT J  79 "
       pdb=" C2'  DT J  79 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  ... (remaining 13718 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 17560
        0.99 -     1.98: 1512
        1.98 -     2.98: 546
        2.98 -     3.97: 27
        3.97 -     4.96: 11
  Bond angle restraints: 19656
  Sorted by residual:
  angle pdb=" N3   DT I  57 "
        pdb=" C4   DT I  57 "
        pdb=" O4   DT I  57 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.90e+01
  angle pdb=" N3   DT J  89 "
        pdb=" C4   DT J  89 "
        pdb=" O4   DT J  89 "
      ideal   model   delta    sigma   weight residual
     119.90  122.49   -2.59 6.00e-01 2.78e+00 1.87e+01
  angle pdb=" N3   DT J  50 "
        pdb=" C4   DT J  50 "
        pdb=" O4   DT J  50 "
      ideal   model   delta    sigma   weight residual
     119.90  122.49   -2.59 6.00e-01 2.78e+00 1.86e+01
  angle pdb=" N3   DT J  51 "
        pdb=" C4   DT J  51 "
        pdb=" O4   DT J  51 "
      ideal   model   delta    sigma   weight residual
     119.90  122.47   -2.57 6.00e-01 2.78e+00 1.83e+01
  angle pdb=" N3   DT I  46 "
        pdb=" C4   DT I  46 "
        pdb=" O4   DT I  46 "
      ideal   model   delta    sigma   weight residual
     119.90  122.46   -2.56 6.00e-01 2.78e+00 1.83e+01
  ... (remaining 19651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.41: 6418
       35.41 -    70.82: 1173
       70.82 -   106.22: 19
      106.22 -   141.63: 2
      141.63 -   177.04: 1
  Dihedral angle restraints: 7613
    sinusoidal: 4818
      harmonic: 2795
  Sorted by residual:
  dihedral pdb=" C4'  DT J  57 "
           pdb=" C3'  DT J  57 "
           pdb=" O3'  DT J  57 "
           pdb=" P    DT J  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.04 -177.04     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  ILE M  32 "
           pdb=" C   ILE M  32 "
           pdb=" N   GLU M  33 "
           pdb=" CA  GLU M  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.71   19.29     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" C4'  DG J  94 "
           pdb=" C3'  DG J  94 "
           pdb=" O3'  DG J  94 "
           pdb=" P    DG J  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   85.73  134.27     1      3.50e+01 8.16e-04 1.33e+01
  ... (remaining 7610 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1692
       0.044 -    0.089: 430
       0.089 -    0.133: 126
       0.133 -    0.178: 0
       0.178 -    0.222: 1
  Chirality restraints: 2249
  Sorted by residual:
  chirality pdb=" CA  GLU G  61 "
            pdb=" N   GLU G  61 "
            pdb=" C   GLU G  61 "
            pdb=" CB  GLU G  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ILE M  31 "
            pdb=" N   ILE M  31 "
            pdb=" C   ILE M  31 "
            pdb=" CB  ILE M  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE C  79 "
            pdb=" N   ILE C  79 "
            pdb=" C   ILE C  79 "
            pdb=" CB  ILE C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  ... (remaining 2246 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.023 5.00e-02 4.00e+02   3.48e-02 1.93e+00
        pdb=" N   PRO G  80 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO C  80 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS G  36 "   -0.006 2.00e-02 2.50e+03   1.11e-02 1.23e+00
        pdb=" C   LYS G  36 "    0.019 2.00e-02 2.50e+03
        pdb=" O   LYS G  36 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY G  37 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 295
        2.67 -     3.23: 10886
        3.23 -     3.78: 22633
        3.78 -     4.34: 28912
        4.34 -     4.90: 43078
  Nonbonded interactions: 105804
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  95 "
            pdb=" N2   DG J  53 "
     model   vdw
     2.109 2.496
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   CYS M  18 "
            pdb=" N   GLY M  22 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   LEU N  80 "
            pdb=" NZ  LYS N  85 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   SER N  41 "
            pdb=" OG  SER N  44 "
     model   vdw
     2.308 3.040
  ... (remaining 105799 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 40 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 100)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 31 through 120)
  selection = (chain 'H' and resid 31 through 120)
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.270
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
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      :  0.005   0.037  13739  Z= 0.465
  Angle     :  0.656  10.916  19674  Z= 0.580
  Chirality :  0.042   0.222   2249
  Planarity :  0.003   0.035   1584
  Dihedral  : 25.414 177.041   5803
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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:  2.37 (0.28), residues: 938
  helix:  2.71 (0.21), residues: 601
  sheet: -0.27 (1.64), residues: 10
  loop : -0.60 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  81 
 TYR   0.015   0.001   TYR A  54 
 PHE   0.007   0.001   PHE N  71 
 TRP   0.001   0.000   TRP N  17 
 HIS   0.003   0.000   HIS D 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00493 /  0.47 (13723)
  covalent geometry    : angle       0.64630 /  0.58 (19656)
  hydrogen bonds       : bond        0.12125 /  8.03 (  765)
  hydrogen bonds       : angle       4.07004 /  2.88 ( 1952)
  metal coordination   : bond        0.00797 /  0.44 (   16)
  metal coordination   : angle       3.73165 /  2.70 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.348 
Fit side-chains
REVERT: D   39 TYR cc_start: 0.6427 (t80) cc_final: 0.6124 (t80)
REVERT: D  105 LYS cc_start: 0.7302 (ptpt) cc_final: 0.7038 (ptpt)
REVERT: M   17 MET cc_start: 0.4458 (pmm) cc_final: 0.2714 (pmm)
REVERT: M   60 VAL cc_start: 0.7224 (t) cc_final: 0.7018 (t)
REVERT: N   65 LYS cc_start: 0.7703 (ptmm) cc_final: 0.7246 (mtpt)
REVERT: N  106 PHE cc_start: 0.5470 (m-80) cc_final: 0.4616 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1466
  time to fit residues: 32.6679
Evaluate side-chains
  144 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN
H  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.156629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.116456 restraints weight = 24353.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.58
r_work: 0.3338 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13739  Z= 0.145
  Angle     :  0.562   8.533  19674  Z= 0.343
  Chirality :  0.041   0.231   2249
  Planarity :  0.004   0.033   1584
  Dihedral  : 28.824 175.256   3899
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  6.47 %
    Favored  : 92.67 %
  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:  2.44 (0.28), residues: 938
  helix:  2.72 (0.21), residues: 611
  sheet:  None (None), residues: 0
  loop : -0.61 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  81 
 TYR   0.018   0.001   TYR A  54 
 PHE   0.007   0.001   PHE B  61 
 TRP   0.008   0.002   TRP N  17 
 HIS   0.003   0.001   HIS N  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.15 (13723)
  covalent geometry    : angle       0.55351 /  0.34 (19656)
  hydrogen bonds       : bond        0.05340 /  3.76 (  765)
  hydrogen bonds       : angle       2.82826 /  2.04 ( 1952)
  metal coordination   : bond        0.00704 /  0.46 (   16)
  metal coordination   : angle       3.19028 /  2.31 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.344 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.6979 (m-30) cc_final: 0.6732 (t0)
REVERT: D   30 ARG cc_start: 0.3928 (ptp-110) cc_final: 0.3707 (mmt-90)
REVERT: D   39 TYR cc_start: 0.7280 (t80) cc_final: 0.7017 (t80)
REVERT: E   76 GLN cc_start: 0.8193 (pp30) cc_final: 0.7889 (pt0)
REVERT: F   91 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (ttpp)
REVERT: H   59 MET cc_start: 0.8711 (mmt) cc_final: 0.8313 (mmt)
REVERT: M   17 MET cc_start: 0.3780 (pmm) cc_final: 0.2896 (pmm)
REVERT: M   60 VAL cc_start: 0.7314 (t) cc_final: 0.7067 (t)
REVERT: N   57 MET cc_start: 0.4944 (tpp) cc_final: 0.3490 (ttm)
REVERT: N   65 LYS cc_start: 0.7236 (ptmm) cc_final: 0.6399 (mtmt)
REVERT: N  106 PHE cc_start: 0.6195 (m-80) cc_final: 0.5755 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 142
  average time/residue: 0.1304
  time to fit residues: 25.8787
Evaluate side-chains
  139 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   44 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   chunk 71 optimal weight:   40.0000
   chunk 100 optimal weight:    0.7980
   overall best weight:    2.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.152519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.110660 restraints weight = 23920.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.53
r_work: 0.3235 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13739  Z= 0.152
  Angle     :  0.585   6.804  19674  Z= 0.344
  Chirality :  0.043   0.231   2249
  Planarity :  0.004   0.033   1584
  Dihedral  : 29.607 176.437   3899
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.16 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.27), residues: 938
  helix:  2.56 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop : -0.92 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  89 
 TYR   0.033   0.002   TYR M  46 
 PHE   0.010   0.002   PHE N 106 
 TRP   0.011   0.003   TRP N  17 
 HIS   0.005   0.001   HIS D 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.15 (13723)
  covalent geometry    : angle       0.57885 /  0.34 (19656)
  hydrogen bonds       : bond        0.05912 /  4.17 (  765)
  hydrogen bonds       : angle       2.76187 /  1.98 ( 1952)
  metal coordination   : bond        0.01060 /  0.72 (   16)
  metal coordination   : angle       2.80347 /  1.99 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.364 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7014 (m-30) cc_final: 0.6791 (t0)
REVERT: M   60 VAL cc_start: 0.7455 (t) cc_final: 0.7150 (t)
REVERT: N   57 MET cc_start: 0.4866 (tpp) cc_final: 0.3483 (ttm)
REVERT: N   65 LYS cc_start: 0.7018 (ptmm) cc_final: 0.6183 (mtmt)
REVERT: N  106 PHE cc_start: 0.6192 (m-80) cc_final: 0.5897 (m-10)
  outliers start: 10
  outliers final: 7
  residues processed: 136
  average time/residue: 0.1234
  time to fit residues: 23.4425
Evaluate side-chains
  137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   44 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 107 optimal weight:   20.0000
   chunk 90 optimal weight:   20.0000
   chunk 38 optimal weight:    7.9990
   chunk 115 optimal weight:    8.9990
   chunk 81 optimal weight:   30.0000
   chunk 60 optimal weight:    0.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 106 HIS
G  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.150166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.107354 restraints weight = 23470.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.54
r_work: 0.3188 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13739  Z= 0.183
  Angle     :  0.622   6.792  19674  Z= 0.357
  Chirality :  0.044   0.233   2249
  Planarity :  0.005   0.058   1584
  Dihedral  : 29.795 175.538   3899
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.87 %
    Favored  : 87.30 %
  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:  1.75 (0.27), residues: 938
  helix:  2.32 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop : -1.14 (0.30), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG M  64 
 TYR   0.013   0.002   TYR M  46 
 PHE   0.014   0.002   PHE N 106 
 TRP   0.013   0.003   TRP N  17 
 HIS   0.006   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.18 (13723)
  covalent geometry    : angle       0.61490 /  0.36 (19656)
  hydrogen bonds       : bond        0.06458 /  4.47 (  765)
  hydrogen bonds       : angle       2.90223 /  2.09 ( 1952)
  metal coordination   : bond        0.01607 /  1.09 (   16)
  metal coordination   : angle       3.23706 /  2.26 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.267 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7082 (m-30) cc_final: 0.6761 (t0)
REVERT: H   59 MET cc_start: 0.8812 (mmt) cc_final: 0.8415 (mmt)
REVERT: H  102 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6910 (mt-10)
REVERT: M   17 MET cc_start: 0.3255 (OUTLIER) cc_final: 0.3018 (pmm)
REVERT: M   64 ARG cc_start: 0.6778 (ttp80) cc_final: 0.6536 (ttp80)
REVERT: M   70 ARG cc_start: 0.6986 (tpp-160) cc_final: 0.6407 (ttm110)
REVERT: N   57 MET cc_start: 0.5023 (tpp) cc_final: 0.3342 (ttm)
REVERT: N   65 LYS cc_start: 0.6823 (ptmm) cc_final: 0.6061 (mtmt)
REVERT: N  106 PHE cc_start: 0.6200 (m-80) cc_final: 0.5657 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 139
  average time/residue: 0.1190
  time to fit residues: 23.3327
Evaluate side-chains
  143 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain M residue   17 MET
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   44 VAL
Chi-restraints excluded: chain N residue   64 THR
Chi-restraints excluded: chain N residue   99 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 108 optimal weight:   10.0000
   chunk 80 optimal weight:   30.0000
   chunk 49 optimal weight:    0.9980
   chunk 74 optimal weight:   30.0000
   chunk 28 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  38 ASN
H 106 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.151886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.108662 restraints weight = 23772.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.79
r_work: 0.3210 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13739  Z= 0.126
  Angle     :  0.541   5.980  19674  Z= 0.321
  Chirality :  0.041   0.208   2249
  Planarity :  0.003   0.036   1584
  Dihedral  : 29.731 175.699   3899
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.23 %
    Favored  : 87.55 %
  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:  2.17 (0.28), residues: 938
  helix:  2.66 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop : -1.01 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  30 
 TYR   0.009   0.001   TYR A  54 
 PHE   0.009   0.001   PHE B  61 
 TRP   0.008   0.002   TRP N  17 
 HIS   0.006   0.001   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00203 /  0.13 (13723)
  covalent geometry    : angle       0.53491 /  0.32 (19656)
  hydrogen bonds       : bond        0.05156 /  3.66 (  765)
  hydrogen bonds       : angle       2.69381 /  1.94 ( 1952)
  metal coordination   : bond        0.01021 /  0.70 (   16)
  metal coordination   : angle       2.80234 /  1.81 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.402 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7136 (m-30) cc_final: 0.6848 (t0)
REVERT: H   90 GLU cc_start: 0.7956 (mp0) cc_final: 0.7449 (mp0)
REVERT: H  102 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6780 (mt-10)
REVERT: M   17 MET cc_start: 0.3678 (pmm) cc_final: 0.3385 (pmm)
REVERT: M   70 ARG cc_start: 0.6833 (tpp-160) cc_final: 0.6170 (ttm110)
REVERT: N   57 MET cc_start: 0.5054 (tpp) cc_final: 0.3683 (ttm)
REVERT: N   65 LYS cc_start: 0.7010 (ptmm) cc_final: 0.6383 (mtmt)
REVERT: N  106 PHE cc_start: 0.5997 (m-80) cc_final: 0.5600 (m-80)
  outliers start: 10
  outliers final: 9
  residues processed: 133
  average time/residue: 0.1123
  time to fit residues: 21.6507
Evaluate side-chains
  135 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain M residue   44 VAL
Chi-restraints excluded: chain N residue   64 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 72 optimal weight:   50.0000
   chunk 80 optimal weight:   30.0000
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   chunk 86 optimal weight:   40.0000
   chunk 2 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   chunk 75 optimal weight:   30.0000
   chunk 42 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.150885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.109031 restraints weight = 23528.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.58
r_work: 0.3209 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13739  Z= 0.151
  Angle     :  0.562   6.048  19674  Z= 0.330
  Chirality :  0.041   0.224   2249
  Planarity :  0.004   0.037   1584
  Dihedral  : 29.785 175.911   3899
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.97 %
    Favored  : 86.20 %
  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:  2.06 (0.28), residues: 938
  helix:  2.59 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop : -1.08 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG M  64 
 TYR   0.010   0.001   TYR H  37 
 PHE   0.012   0.001   PHE N 106 
 TRP   0.009   0.002   TRP N  17 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.15 (13723)
  covalent geometry    : angle       0.55590 /  0.33 (19656)
  hydrogen bonds       : bond        0.05585 /  3.92 (  765)
  hydrogen bonds       : angle       2.73926 /  1.97 ( 1952)
  metal coordination   : bond        0.01224 /  0.83 (   16)
  metal coordination   : angle       2.85480 /  1.82 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.347 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7132 (m-30) cc_final: 0.6836 (t0)
REVERT: H   90 GLU cc_start: 0.7935 (mp0) cc_final: 0.7439 (mp0)
REVERT: H  102 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6652 (mt-10)
REVERT: M   17 MET cc_start: 0.2991 (OUTLIER) cc_final: 0.2708 (pmm)
REVERT: M   70 ARG cc_start: 0.6959 (tpp-160) cc_final: 0.6361 (ttm110)
REVERT: N   57 MET cc_start: 0.5075 (tpp) cc_final: 0.3515 (ttm)
REVERT: N   65 LYS cc_start: 0.7060 (ptmm) cc_final: 0.6352 (mtmt)
REVERT: N  106 PHE cc_start: 0.5951 (m-80) cc_final: 0.5594 (m-80)
  outliers start: 15
  outliers final: 14
  residues processed: 131
  average time/residue: 0.1032
  time to fit residues: 19.6332
Evaluate side-chains
  139 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain M residue   17 MET
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain M residue   44 VAL
Chi-restraints excluded: chain N residue   64 THR
Chi-restraints excluded: chain N residue   99 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 54 optimal weight:    0.2980
   chunk 117 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 83 optimal weight:   50.0000
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 92 optimal weight:   30.0000
   chunk 42 optimal weight:    0.9980
   chunk 76 optimal weight:   30.0000
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.151635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.108274 restraints weight = 23590.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.83
r_work: 0.3206 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13739  Z= 0.125
  Angle     :  0.540   6.005  19674  Z= 0.320
  Chirality :  0.041   0.209   2249
  Planarity :  0.003   0.037   1584
  Dihedral  : 29.761 175.967   3899
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.09 %
    Favored  : 86.08 %
  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:  2.19 (0.28), residues: 938
  helix:  2.69 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop : -1.04 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG M  64 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.009   0.001   PHE N 106 
 TRP   0.007   0.002   TRP N  17 
 HIS   0.003   0.001   HIS M  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00202 /  0.12 (13723)
  covalent geometry    : angle       0.53422 /  0.32 (19656)
  hydrogen bonds       : bond        0.05142 /  3.65 (  765)
  hydrogen bonds       : angle       2.69444 /  1.94 ( 1952)
  metal coordination   : bond        0.01180 /  0.85 (   16)
  metal coordination   : angle       2.76012 /  1.74 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.362 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7109 (m-30) cc_final: 0.6826 (t0)
REVERT: H   90 GLU cc_start: 0.7987 (mp0) cc_final: 0.7548 (mp0)
REVERT: H  102 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6624 (mt-10)
REVERT: M   17 MET cc_start: 0.3007 (OUTLIER) cc_final: 0.2736 (pmm)
REVERT: M   70 ARG cc_start: 0.6949 (tpp-160) cc_final: 0.6353 (ttm110)
REVERT: N   57 MET cc_start: 0.5009 (tpp) cc_final: 0.3731 (ttm)
REVERT: N   65 LYS cc_start: 0.6992 (ptmm) cc_final: 0.6260 (mtmt)
REVERT: N  106 PHE cc_start: 0.5948 (m-80) cc_final: 0.5605 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1094
  time to fit residues: 20.4717
Evaluate side-chains
  135 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain M residue   17 MET
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain M residue   44 VAL
Chi-restraints excluded: chain N residue   64 THR
Chi-restraints excluded: chain N residue   99 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0270
   chunk 78 optimal weight:   30.0000
   chunk 81 optimal weight:   30.0000
   chunk 5 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0770
   chunk 30 optimal weight:    0.9980
   chunk 82 optimal weight:   40.0000
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.0200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  38 ASN
M  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.152395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.109483 restraints weight = 23516.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.75
r_work: 0.3230 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13739  Z= 0.119
  Angle     :  0.520   5.724  19674  Z= 0.312
  Chirality :  0.040   0.209   2249
  Planarity :  0.003   0.037   1584
  Dihedral  : 29.686 176.550   3899
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.70 %
    Favored  : 85.47 %
  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:  2.31 (0.28), residues: 938
  helix:  2.76 (0.21), residues: 611
  sheet:  None (None), residues: 0
  loop : -0.97 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  76 
 TYR   0.008   0.001   TYR A  54 
 PHE   0.010   0.001   PHE N 106 
 TRP   0.008   0.002   TRP N  17 
 HIS   0.002   0.001   HIS M  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00188 /  0.12 (13723)
  covalent geometry    : angle       0.51336 /  0.31 (19656)
  hydrogen bonds       : bond        0.04774 /  3.41 (  765)
  hydrogen bonds       : angle       2.59532 /  1.87 ( 1952)
  metal coordination   : bond        0.00971 /  0.69 (   16)
  metal coordination   : angle       2.71060 /  1.65 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.272 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7063 (m-30) cc_final: 0.6817 (t0)
REVERT: H   90 GLU cc_start: 0.7936 (mp0) cc_final: 0.7638 (mp0)
REVERT: H  102 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6647 (mt-10)
REVERT: M   17 MET cc_start: 0.3286 (OUTLIER) cc_final: 0.2943 (pmm)
REVERT: N   57 MET cc_start: 0.4961 (tpp) cc_final: 0.3763 (ttm)
REVERT: N   65 LYS cc_start: 0.7109 (ptmm) cc_final: 0.6437 (mtmt)
REVERT: N  106 PHE cc_start: 0.6101 (m-80) cc_final: 0.5784 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 134
  average time/residue: 0.1181
  time to fit residues: 22.4526
Evaluate side-chains
  138 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain M residue   17 MET
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain M residue   44 VAL
Chi-restraints excluded: chain M residue   76 GLN
Chi-restraints excluded: chain N residue   64 THR
Chi-restraints excluded: chain N residue   99 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 118 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0970
   chunk 82 optimal weight:   40.0000
   chunk 115 optimal weight:    6.9990
   chunk 93 optimal weight:   30.0000
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.151165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.109309 restraints weight = 23594.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.46
r_work: 0.3219 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13739  Z= 0.148
  Angle     :  0.552   5.894  19674  Z= 0.325
  Chirality :  0.041   0.223   2249
  Planarity :  0.004   0.037   1584
  Dihedral  : 29.772 177.870   3899
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.31 %
    Favored  : 84.86 %
  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:  2.13 (0.28), residues: 938
  helix:  2.64 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop : -1.05 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  89 
 TYR   0.010   0.001   TYR H  37 
 PHE   0.012   0.001   PHE N 106 
 TRP   0.008   0.002   TRP N  17 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.15 (13723)
  covalent geometry    : angle       0.54621 /  0.33 (19656)
  hydrogen bonds       : bond        0.05381 /  3.80 (  765)
  hydrogen bonds       : angle       2.70813 /  1.95 ( 1952)
  metal coordination   : bond        0.01230 /  0.86 (   16)
  metal coordination   : angle       2.68565 /  1.65 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.383 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7096 (m-30) cc_final: 0.6813 (t0)
REVERT: H   90 GLU cc_start: 0.7957 (mp0) cc_final: 0.7604 (mp0)
REVERT: H  102 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6797 (mt-10)
REVERT: M   17 MET cc_start: 0.2916 (OUTLIER) cc_final: 0.2656 (pmm)
REVERT: M   24 TYR cc_start: 0.4312 (OUTLIER) cc_final: 0.3904 (t80)
REVERT: N   57 MET cc_start: 0.5026 (tpp) cc_final: 0.3769 (ttm)
REVERT: N   65 LYS cc_start: 0.7089 (ptmm) cc_final: 0.6369 (mtmt)
REVERT: N  106 PHE cc_start: 0.6075 (m-80) cc_final: 0.5801 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 131
  average time/residue: 0.1169
  time to fit residues: 22.3638
Evaluate side-chains
  138 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   87 VAL
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain M residue   17 MET
Chi-restraints excluded: chain M residue   24 TYR
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain M residue   44 VAL
Chi-restraints excluded: chain N residue   64 THR
Chi-restraints excluded: chain N residue   99 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 117 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9980
   chunk 81 optimal weight:   30.0000
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  38 ASN
** M  76 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 = 0.4075 r_free = 0.4075 target = 0.151349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.109420 restraints weight = 23670.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.54
r_work: 0.3217 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13739  Z= 0.134
  Angle     :  0.541   5.921  19674  Z= 0.321
  Chirality :  0.040   0.217   2249
  Planarity :  0.004   0.037   1584
  Dihedral  : 29.778 178.024   3899
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.80 %
    Favored  : 84.37 %
  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:  2.15 (0.28), residues: 938
  helix:  2.65 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop : -1.04 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  89 
 TYR   0.009   0.001   TYR H  37 
 PHE   0.011   0.001   PHE N 106 
 TRP   0.007   0.002   TRP N  17 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.13 (13723)
  covalent geometry    : angle       0.53542 /  0.32 (19656)
  hydrogen bonds       : bond        0.05237 /  3.71 (  765)
  hydrogen bonds       : angle       2.68770 /  1.93 ( 1952)
  metal coordination   : bond        0.01202 /  0.85 (   16)
  metal coordination   : angle       2.69156 /  1.66 (   18)

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.283 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7084 (m-30) cc_final: 0.6810 (t0)
REVERT: H   90 GLU cc_start: 0.7975 (mp0) cc_final: 0.7622 (mp0)
REVERT: H  102 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6676 (mt-10)
REVERT: M   17 MET cc_start: 0.2943 (OUTLIER) cc_final: 0.2668 (pmm)
REVERT: M   24 TYR cc_start: 0.4420 (OUTLIER) cc_final: 0.4045 (t80)
REVERT: N   57 MET cc_start: 0.5007 (tpp) cc_final: 0.3750 (ttm)
REVERT: N   65 LYS cc_start: 0.7094 (ptmm) cc_final: 0.6363 (mtmt)
REVERT: N  106 PHE cc_start: 0.6099 (m-80) cc_final: 0.5821 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1133
  time to fit residues: 21.1528
Evaluate side-chains
  137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   97 LEU
Chi-restraints excluded: chain M residue   17 MET
Chi-restraints excluded: chain M residue   24 TYR
Chi-restraints excluded: chain M residue   30 THR
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain M residue   44 VAL
Chi-restraints excluded: chain N residue   64 THR
Chi-restraints excluded: chain N residue   99 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 82 optimal weight:   40.0000
   chunk 18 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 87 optimal weight:   20.0000
   chunk 88 optimal weight:   30.0000
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.150427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.106954 restraints weight = 23375.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.77
r_work: 0.3178 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13739  Z= 0.146
  Angle     :  0.566   6.066  19674  Z= 0.332
  Chirality :  0.041   0.221   2249
  Planarity :  0.004   0.037   1584
  Dihedral  : 29.886 179.529   3899
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.92 %
    Favored  : 84.13 %
  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:  2.01 (0.27), residues: 938
  helix:  2.55 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -1.13 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  89 
 TYR   0.010   0.001   TYR H  37 
 PHE   0.015   0.001   PHE N 106 
 TRP   0.011   0.003   TRP N  17 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.15 (13723)
  covalent geometry    : angle       0.56022 /  0.33 (19656)
  hydrogen bonds       : bond        0.05642 /  3.97 (  765)
  hydrogen bonds       : angle       2.76083 /  1.99 ( 1952)
  metal coordination   : bond        0.01380 /  0.98 (   16)
  metal coordination   : angle       2.77727 /  1.74 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2838.82 seconds
wall clock time: 49 minutes 9.65 seconds (2949.65 seconds total)