Starting phenix.real_space_refine
on Wed Feb  4 18:03:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ge4_51289/02_2026/9ge4_51289.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ge4_51289/02_2026/9ge4_51289.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ge4_51289/02_2026/9ge4_51289.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ge4_51289/02_2026/9ge4_51289.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ge4_51289/02_2026/9ge4_51289.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ge4_51289/02_2026/9ge4_51289.cif"
  }
  resolution = 3.52
  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=   0.019
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: 5
    Type Number    sf(0)   Gaussians
     P     304      5.49       5
     S      14      5.16       5
     C    6662      2.51       5
     N    2265      2.21       5
     O    2876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12121
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "K"
      Number of atoms: 3132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 3132
          Classifications: {'DNA': 152}
          Link IDs: {'rna3p': 151}
    Chain: "L"
      Number of atoms: 3100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 3100
          Classifications: {'DNA': 152}
          Link IDs: {'rna3p': 151}
    Chain: "M"
      Number of atoms: 739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 739
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "N"
      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: "O"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 803
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 3, 'TRANS': 102}
    Chain: "P"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "Q"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "R"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "S"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 819
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 3, 'TRANS': 104}
    Chain: "T"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 720
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
  Time building chain proxies: 1.96, per 1000 atoms: 0.16
  Number of scatterers: 12121
  At special positions: 0
  Unit cell: (117.875, 130.134, 115.046, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     304     15.00
     O    2876      8.00
     N    2265      7.00
     C    6662      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: 0.61
  Conformation dependent library (CDL) restraints added in 328.8 milliseconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      66.8% alpha, 2.1% beta
      127 base pairs and 258 stacking pairs defined.
    Time for finding SS restraints: 1.65
  Creating SS restraints...
    Processing helix  chain 'M' and resid 45 through 55
      removed outlier: 3.908A  pdb=" N   ILE M  51 " --> pdb=" O   ALA M  47 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ARG M  52 " --> pdb=" O   LEU M  48 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 63 through 76
      removed outlier: 3.602A  pdb=" N   GLN M  76 " --> pdb=" O   ARG M  72 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 85 through 114
      removed outlier: 3.590A  pdb=" N   VAL M  89 " --> pdb=" O   GLN M  85 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   MET M  90 " --> pdb=" O   SER M  86 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA M  95 " --> pdb=" O   ALA M  91 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU M 109 " --> pdb=" O   GLU M 105 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   CYS M 110 " --> pdb=" O   ASP M 106 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 120 through 132
    Processing helix  chain 'N' and resid 24 through 29
    Processing helix  chain 'N' and resid 30 through 42
    Processing helix  chain 'N' and resid 49 through 76
      removed outlier: 3.572A  pdb=" N   GLY N  56 " --> pdb=" O   GLU N  52 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ASP N  68 " --> pdb=" O   ASN N  64 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA N  76 " --> pdb=" O   TYR N  72 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 82 through 93
      removed outlier: 4.022A  pdb=" N   GLN N  93 " --> pdb=" O   ALA N  89 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 16 through 22
      removed outlier: 3.603A  pdb=" N   ARG O  20 " --> pdb=" O   SER O  16 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 28 through 33
      removed outlier: 3.919A  pdb=" N   ARG O  32 " --> pdb=" O   GLY O  28 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 34 through 37
    Processing helix  chain 'O' and resid 44 through 52
      removed outlier: 4.094A  pdb=" N   ALA O  48 " --> pdb=" O   VAL O  44 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ALA O  49 " --> pdb=" O   GLY O  45 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL O  50 " --> pdb=" O   ALA O  46 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 64 through 69
    Processing helix  chain 'O' and resid 70 through 74
    Processing helix  chain 'P' and resid 37 through 49
      removed outlier: 3.952A  pdb=" N   TYR P  42 " --> pdb=" O   SER P  38 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN P  47 " --> pdb=" O   LYS P  43 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 55 through 85
      removed outlier: 3.720A  pdb=" N   GLY P  60 " --> pdb=" O   SER P  56 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE P  61 " --> pdb=" O   LYS P  57 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER P  78 " --> pdb=" O   ALA P  74 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ARG P  79 " --> pdb=" O   GLY P  75 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU P  80 " --> pdb=" O   GLU P  76 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA P  81 " --> pdb=" O   ALA P  77 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 90 through 101
    Processing helix  chain 'P' and resid 103 through 123
      removed outlier: 3.976A  pdb=" N   LYS P 108 " --> pdb=" O   GLY P 104 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER P 112 " --> pdb=" O   LYS P 108 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 44 through 55
      removed outlier: 3.520A  pdb=" N   ARG Q  52 " --> pdb=" O   LEU Q  48 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 63 through 77
      removed outlier: 3.896A  pdb=" N   ASP Q  77 " --> pdb=" O   GLU Q  73 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 87 through 114
      removed outlier: 3.520A  pdb=" N   ALA Q  95 " --> pdb=" O   ALA Q  91 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ALA Q  98 " --> pdb=" O   GLU Q  94 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY Q 102 " --> pdb=" O   ALA Q  98 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU Q 109 " --> pdb=" O   GLU Q 105 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   CYS Q 110 " --> pdb=" O   ASP Q 106 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 120 through 131
      removed outlier: 3.729A  pdb=" N   ILE Q 124 " --> pdb=" O   MET Q 120 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU Q 126 " --> pdb=" O   LYS Q 122 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG Q 129 " --> pdb=" O   GLN Q 125 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 24 through 29
    Processing helix  chain 'R' and resid 30 through 42
    Processing helix  chain 'R' and resid 49 through 76
      removed outlier: 3.536A  pdb=" N   GLU R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   GLY R  56 " --> pdb=" O   GLU R  52 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL R  57 " --> pdb=" O   GLU R  53 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ASP R  68 " --> pdb=" O   ASN R  64 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA R  76 " --> pdb=" O   TYR R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 82 through 93
    Processing helix  chain 'S' and resid 16 through 22
    Processing helix  chain 'S' and resid 26 through 35
    Processing helix  chain 'S' and resid 45 through 62
      removed outlier: 3.767A  pdb=" N   ALA S  49 " --> pdb=" O   GLY S  45 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   TYR S  51 " --> pdb=" O   THR S  47 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA S  54 " --> pdb=" O   VAL S  50 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE S  55 " --> pdb=" O   TYR S  51 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   TYR S  58 " --> pdb=" O   ALA S  54 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 63 through 71
    Processing helix  chain 'S' and resid 80 through 88
      removed outlier: 3.785A  pdb=" N   LEU S  84 " --> pdb=" O   THR S  80 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU S  86 " --> pdb=" O   ARG S  82 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 92 through 97
    Processing helix  chain 'T' and resid 37 through 49
      removed outlier: 3.613A  pdb=" N   TYR T  42 " --> pdb=" O   SER T  38 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 55 through 84
      removed outlier: 4.007A  pdb=" N   ILE T  61 " --> pdb=" O   LYS T  57 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   MET T  62 " --> pdb=" O   ALA T  58 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ASN T  67 " --> pdb=" O   ASN T  63 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 91 through 102
      removed outlier: 4.053A  pdb=" N   ALA T  97 " --> pdb=" O   GLU T  93 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 104 through 122
      removed outlier: 3.788A  pdb=" N   LYS T 108 " --> pdb=" O   GLY T 104 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS T 116 " --> pdb=" O   SER T 112 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   THR T 119 " --> pdb=" O   THR T 115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84
      removed outlier: 6.616A  pdb=" N   ARG M  83 " --> pdb=" O   VAL N  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'N' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'O' and resid 100 through 102
    Processing sheet with id=AA5, first strand: chain 'Q' and resid 83 through 84
      removed outlier: 7.063A  pdb=" N   ARG Q  83 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'Q' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'S' and resid 77 through 78

    308 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      320 hydrogen bonds
      640 hydrogen bond angles
      0 basepair planarities
      127 basepair parallelities
      258 stacking parallelities
  Total time for adding SS restraints: 1.94

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1526
        1.32 -     1.44: 4627
        1.44 -     1.57: 6163
        1.57 -     1.69: 617
        1.69 -     1.82: 24
  Bond restraints: 12957
  Sorted by residual:
  bond pdb=" CG  HIS O  83 "
       pdb=" CD2 HIS O  83 "
    ideal  model  delta    sigma   weight residual
    1.354  1.280  0.074 1.10e-02 8.26e+03 4.49e+01
  bond pdb=" C   THR O  80 "
       pdb=" N   PRO O  81 "
    ideal  model  delta    sigma   weight residual
    1.337  1.389 -0.052 1.11e-02 8.12e+03 2.21e+01
  bond pdb=" CG  HIS R  75 "
       pdb=" CD2 HIS R  75 "
    ideal  model  delta    sigma   weight residual
    1.354  1.304  0.050 1.10e-02 8.26e+03 2.05e+01
  bond pdb=" CG  HIS S  31 "
       pdb=" CD2 HIS S  31 "
    ideal  model  delta    sigma   weight residual
    1.354  1.305  0.049 1.10e-02 8.26e+03 2.01e+01
  bond pdb=" CG  HIS S  83 "
       pdb=" CD2 HIS S  83 "
    ideal  model  delta    sigma   weight residual
    1.354  1.314  0.040 1.10e-02 8.26e+03 1.30e+01
  ... (remaining 12952 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 16543
        2.98 -     5.95: 2029
        5.95 -     8.93: 195
        8.93 -    11.90: 21
       11.90 -    14.88: 9
  Bond angle restraints: 18797
  Sorted by residual:
  angle pdb=" N   LEU O  64 "
        pdb=" CA  LEU O  64 "
        pdb=" CB  LEU O  64 "
      ideal   model   delta    sigma   weight residual
     110.49  125.37  -14.88 1.69e+00 3.50e-01 7.75e+01
  angle pdb=" O3'  DG K -44 "
        pdb=" P    DT K -43 "
        pdb=" O5'  DT K -43 "
      ideal   model   delta    sigma   weight residual
     104.00   91.73   12.27 1.50e+00 4.44e-01 6.69e+01
  angle pdb=" N   VAL O  50 "
        pdb=" CA  VAL O  50 "
        pdb=" CB  VAL O  50 "
      ideal   model   delta    sigma   weight residual
     112.33  121.59   -9.26 1.19e+00 7.06e-01 6.06e+01
  angle pdb=" CA  VAL S  50 "
        pdb=" CB  VAL S  50 "
        pdb=" CG1 VAL S  50 "
      ideal   model   delta    sigma   weight residual
     110.40  122.72  -12.32 1.70e+00 3.46e-01 5.25e+01
  angle pdb=" CA  VAL O  50 "
        pdb=" CB  VAL O  50 "
        pdb=" CG2 VAL O  50 "
      ideal   model   delta    sigma   weight residual
     110.40  122.60  -12.20 1.70e+00 3.46e-01 5.15e+01
  ... (remaining 18792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.97: 5654
       33.97 -    67.94: 1284
       67.94 -   101.91: 50
      101.91 -   135.88: 0
      135.88 -   169.86: 4
  Dihedral angle restraints: 6992
    sinusoidal: 4837
      harmonic: 2155
  Sorted by residual:
  dihedral pdb=" CA  ILE O  55 "
           pdb=" C   ILE O  55 "
           pdb=" N   LEU O  56 "
           pdb=" CA  LEU O  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.73   33.27     0      5.00e+00 4.00e-02 4.43e+01
  dihedral pdb=" CA  VAL P  98 "
           pdb=" C   VAL P  98 "
           pdb=" N   ARG P  99 "
           pdb=" CA  ARG P  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.00   32.00     0      5.00e+00 4.00e-02 4.10e+01
  dihedral pdb=" CA  THR O  60 "
           pdb=" C   THR O  60 "
           pdb=" N   ALA O  61 "
           pdb=" CA  ALA O  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.88   31.12     0      5.00e+00 4.00e-02 3.87e+01
  ... (remaining 6989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 1666
       0.129 -    0.258: 394
       0.258 -    0.387: 73
       0.387 -    0.516: 9
       0.516 -    0.645: 2
  Chirality restraints: 2144
  Sorted by residual:
  chirality pdb=" P    DT L -81 "
            pdb=" OP1  DT L -81 "
            pdb=" OP2  DT L -81 "
            pdb=" O5'  DT L -81 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.99   -0.64 2.00e-01 2.50e+01 1.04e+01
  chirality pdb=" P    DC K -70 "
            pdb=" OP1  DC K -70 "
            pdb=" OP2  DC K -70 "
            pdb=" O5'  DC K -70 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.94   -0.59 2.00e-01 2.50e+01 8.81e+00
  chirality pdb=" P    DA K  38 "
            pdb=" OP1  DA K  38 "
            pdb=" OP2  DA K  38 "
            pdb=" O5'  DA K  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.79   -0.45 2.00e-01 2.50e+01 5.02e+00
  ... (remaining 2141 not shown)

  Planarity restraints: 1317
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG L -56 "    0.158 2.00e-02 2.50e+03   6.47e-02 1.25e+02
        pdb=" N9   DG L -56 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8   DG L -56 "   -0.060 2.00e-02 2.50e+03
        pdb=" N7   DG L -56 "   -0.048 2.00e-02 2.50e+03
        pdb=" C5   DG L -56 "   -0.032 2.00e-02 2.50e+03
        pdb=" C6   DG L -56 "    0.017 2.00e-02 2.50e+03
        pdb=" O6   DG L -56 "    0.112 2.00e-02 2.50e+03
        pdb=" N1   DG L -56 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG L -56 "   -0.023 2.00e-02 2.50e+03
        pdb=" N2   DG L -56 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3   DG L -56 "   -0.030 2.00e-02 2.50e+03
        pdb=" C4   DG L -56 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG K -14 "   -0.149 2.00e-02 2.50e+03   6.12e-02 1.12e+02
        pdb=" N9   DG K -14 "    0.034 2.00e-02 2.50e+03
        pdb=" C8   DG K -14 "    0.088 2.00e-02 2.50e+03
        pdb=" N7   DG K -14 "    0.049 2.00e-02 2.50e+03
        pdb=" C5   DG K -14 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DG K -14 "   -0.044 2.00e-02 2.50e+03
        pdb=" O6   DG K -14 "   -0.074 2.00e-02 2.50e+03
        pdb=" N1   DG K -14 "   -0.017 2.00e-02 2.50e+03
        pdb=" C2   DG K -14 "    0.008 2.00e-02 2.50e+03
        pdb=" N2   DG K -14 "    0.052 2.00e-02 2.50e+03
        pdb=" N3   DG K -14 "    0.022 2.00e-02 2.50e+03
        pdb=" C4   DG K -14 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT K -35 "   -0.136 2.00e-02 2.50e+03   6.39e-02 1.02e+02
        pdb=" N1   DT K -35 "    0.032 2.00e-02 2.50e+03
        pdb=" C2   DT K -35 "    0.043 2.00e-02 2.50e+03
        pdb=" O2   DT K -35 "    0.049 2.00e-02 2.50e+03
        pdb=" N3   DT K -35 "    0.023 2.00e-02 2.50e+03
        pdb=" C4   DT K -35 "   -0.015 2.00e-02 2.50e+03
        pdb=" O4   DT K -35 "   -0.109 2.00e-02 2.50e+03
        pdb=" C5   DT K -35 "    0.043 2.00e-02 2.50e+03
        pdb=" C7   DT K -35 "    0.030 2.00e-02 2.50e+03
        pdb=" C6   DT K -35 "    0.040 2.00e-02 2.50e+03
  ... (remaining 1314 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 90
        2.62 -     3.19: 9381
        3.19 -     3.76: 19892
        3.76 -     4.33: 28962
        4.33 -     4.90: 40863
  Nonbonded interactions: 99188
  Sorted by model distance:
  nonbonded pdb=" OP1  DG K -13 "
            pdb=" NH2 ARG N  36 "
     model   vdw
     2.050 3.120
  nonbonded pdb=" OE1 GLU Q  50 "
            pdb=" NH1 ARG R  39 "
     model   vdw
     2.117 3.120
  nonbonded pdb=" OP1  DG K  26 "
            pdb=" NZ  LYS R  79 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" N2   DG K  51 "
            pdb=" O2   DC L -51 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OP1  DA L  39 "
            pdb=" CE  LYS O  35 "
     model   vdw
     2.221 3.440
  ... (remaining 99183 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 'M'
  selection = (chain 'Q' and resid 43 through 133)
}
ncs_group {
  reference = (chain 'N' and resid 24 through 102)
  selection = chain 'R'
}
ncs_group {
  reference = (chain 'O' and (resid 13 through 107 or resid 109 through 118))
  selection = (chain 'S' and (resid 13 through 107 or resid 109 through 118))
}
ncs_group {
  reference = (chain 'P' and resid 32 through 123)
  selection = chain 'T'
}

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 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:             7.670
  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:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     10.580
  Find NCS groups from input model:        0.220
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
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      :  0.012   0.093  12957  Z= 0.641
  Angle     :  1.978  14.880  18797  Z= 1.206
  Chirality :  0.117   0.645   2144
  Planarity :  0.028   0.247   1317
  Dihedral  : 27.603 169.856   5604
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  7.65 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  :  7.58 %
    Favored  : 89.35 %
  Cbeta Deviations :  1.73 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

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: -4.02 (0.24), residues: 732
  helix: -2.59 (0.18), residues: 499
  sheet:  None (None), residues: 0
  loop : -2.39 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.058   0.008   ARG R  67 
 TYR   0.104   0.015   TYR O  51 
 PHE   0.053   0.014   PHE P  70 
 HIS   0.021   0.007   HIS R  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.01181 (12957)
  covalent geometry    : angle       1.97783 (18797)
  hydrogen bonds       : bond        0.20935 (  628)
  hydrogen bonds       : angle       7.83408 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   56 LYS cc_start: 0.8953 (mttt) cc_final: 0.8669 (ttpt)
REVERT: M   59 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7777 (pt0)
REVERT: M   87 SER cc_start: 0.9261 (m) cc_final: 0.9042 (t)
REVERT: M   94 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8984 (tp30)
REVERT: N   25 ASN cc_start: 0.9272 (m110) cc_final: 0.9045 (m-40)
REVERT: N   27 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8162 (tm-30)
REVERT: N   74 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8511 (mt-10)
REVERT: O   16 SER cc_start: 0.8626 (t) cc_final: 0.8390 (p)
REVERT: O   84 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7789 (tp)
REVERT: O   85 GLN cc_start: 0.7373 (mt0) cc_final: 0.7154 (mt0)
REVERT: O   91 ASP cc_start: 0.8480 (p0) cc_final: 0.8181 (t70)
REVERT: O   92 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8287 (pm20)
REVERT: P   40 TYR cc_start: 0.8904 (m-80) cc_final: 0.8699 (m-80)
REVERT: P   87 SER cc_start: 0.9149 (m) cc_final: 0.8842 (p)
REVERT: P  116 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8345 (mtpp)
REVERT: Q   41 TYR cc_start: 0.8913 (m-80) cc_final: 0.8608 (m-80)
REVERT: Q   42 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7826 (ttm-80)
REVERT: Q   77 ASP cc_start: 0.9339 (m-30) cc_final: 0.9081 (t0)
REVERT: Q   94 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8554 (tp30)
REVERT: Q  129 ARG cc_start: 0.8676 (ttt-90) cc_final: 0.8284 (ttm110)
REVERT: R   30 THR cc_start: 0.8836 (p) cc_final: 0.8633 (t)
REVERT: R   63 GLU cc_start: 0.9181 (tp30) cc_final: 0.8893 (mt-10)
REVERT: R   84 MET cc_start: 0.8744 (mmm) cc_final: 0.8388 (tpp)
REVERT: S   89 ARG cc_start: 0.9064 (ttt180) cc_final: 0.8753 (tpm170)
REVERT: S  113 LYS cc_start: 0.7645 (tmmm) cc_final: 0.7440 (tppt)
REVERT: T   33 ARG cc_start: 0.7330 (mtm180) cc_final: 0.6750 (mtt90)
REVERT: T   35 GLU cc_start: 0.8955 (tt0) cc_final: 0.8647 (tt0)
REVERT: T   41 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8644 (p)
REVERT: T   59 MET cc_start: 0.8992 (tpp) cc_final: 0.8736 (tpp)
REVERT: T   86 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7885 (tpp80)
REVERT: T   87 SER cc_start: 0.8993 (m) cc_final: 0.8634 (p)
  outliers start: 19
  outliers final: 5
  residues processed: 198
  average time/residue: 0.1391
  time to fit residues: 35.8379
Evaluate side-chains
  151 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   43 VAL
Chi-restraints excluded: chain O residue   84 LEU
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain T residue   41 VAL
Chi-restraints excluded: chain T residue   54 ILE
Chi-restraints excluded: chain T residue   94 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0050
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
N  75 HIS
O  33 HIS
O  83 HIS
P  82 HIS
S  31 HIS
** S  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  85 GLN
T  49 HIS
T  84 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.151410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.110557 restraints weight = 19436.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.113517 restraints weight = 10485.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.115404 restraints weight = 7225.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.116528 restraints weight = 5882.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.117120 restraints weight = 5263.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12957  Z= 0.188
  Angle     :  0.726   7.582  18797  Z= 0.427
  Chirality :  0.043   0.224   2144
  Planarity :  0.005   0.045   1317
  Dihedral  : 31.158 164.337   4167
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  3.83 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.19 %
    Favored  : 82.74 %
  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: -1.82 (0.29), residues: 732
  helix: -0.63 (0.22), residues: 503
  sheet:  None (None), residues: 0
  loop : -2.31 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R  67 
 TYR   0.028   0.003   TYR N  88 
 PHE   0.015   0.002   PHE Q  78 
 HIS   0.005   0.001   HIS S  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12957)
  covalent geometry    : angle       0.72624 (18797)
  hydrogen bonds       : bond        0.05336 (  628)
  hydrogen bonds       : angle       3.36959 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 177
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   93 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7971 (mt-10)
REVERT: P   76 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: Q   86 SER cc_start: 0.9085 (m) cc_final: 0.8802 (m)
REVERT: Q  129 ARG cc_start: 0.8051 (ttt-90) cc_final: 0.7815 (ttm110)
REVERT: T   33 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7325 (mtt90)
REVERT: T   87 SER cc_start: 0.8625 (m) cc_final: 0.8165 (p)
  outliers start: 19
  outliers final: 6
  residues processed: 190
  average time/residue: 0.1296
  time to fit residues: 33.0281
Evaluate side-chains
  149 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 143
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   66 VAL
Chi-restraints excluded: chain T residue   94 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** N  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  85 GLN
P  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.150537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.108452 restraints weight = 19685.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.111306 restraints weight = 10679.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.113103 restraints weight = 7441.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.114108 restraints weight = 6107.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.114756 restraints weight = 5515.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12957  Z= 0.204
  Angle     :  0.695   9.265  18797  Z= 0.407
  Chirality :  0.040   0.232   2144
  Planarity :  0.005   0.053   1317
  Dihedral  : 31.056 166.611   4160
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.19 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 15.81 %
    Favored  : 79.68 %
  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: -1.21 (0.30), residues: 732
  helix: -0.06 (0.24), residues: 497
  sheet:  None (None), residues: 0
  loop : -2.33 (0.35), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG O  20 
 TYR   0.036   0.003   TYR P  83 
 PHE   0.038   0.002   PHE Q  78 
 HIS   0.003   0.001   HIS S 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (12957)
  covalent geometry    : angle       0.69452 (18797)
  hydrogen bonds       : bond        0.05164 (  628)
  hydrogen bonds       : angle       3.20623 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   52 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8170 (ttm-80)
REVERT: N   88 TYR cc_start: 0.7918 (m-80) cc_final: 0.7635 (m-80)
REVERT: P   76 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: Q   73 GLU cc_start: 0.7381 (tt0) cc_final: 0.7103 (tt0)
REVERT: Q   86 SER cc_start: 0.9041 (m) cc_final: 0.8807 (m)
REVERT: Q   94 GLU cc_start: 0.7790 (tp30) cc_final: 0.7413 (tp30)
REVERT: Q  129 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7595 (mtp-110)
REVERT: S   24 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8104 (mm-40)
REVERT: T   86 ARG cc_start: 0.8454 (tpp80) cc_final: 0.8024 (ttm-80)
REVERT: T   87 SER cc_start: 0.8573 (m) cc_final: 0.8142 (p)
REVERT: T   93 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7295 (mt-10)
  outliers start: 28
  outliers final: 20
  residues processed: 169
  average time/residue: 0.1256
  time to fit residues: 28.5910
Evaluate side-chains
  152 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   80 THR
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   30 THR
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain P residue  122 THR
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   12 THR
Chi-restraints excluded: chain S residue   23 LEU
Chi-restraints excluded: chain S residue   74 LEU
Chi-restraints excluded: chain S residue   85 GLN
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   36 SER
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   54 ILE
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** N  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.146646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.104019 restraints weight = 19439.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106783 restraints weight = 10587.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.108538 restraints weight = 7433.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.109564 restraints weight = 6123.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.110094 restraints weight = 5531.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12957  Z= 0.187
  Angle     :  0.657   9.987  18797  Z= 0.387
  Chirality :  0.038   0.198   2144
  Planarity :  0.005   0.046   1317
  Dihedral  : 30.972 167.477   4160
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.05 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 15.32 %
    Favored  : 79.52 %
  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: -0.95 (0.30), residues: 732
  helix:  0.17 (0.24), residues: 498
  sheet:  None (None), residues: 0
  loop : -2.30 (0.35), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R  92 
 TYR   0.044   0.002   TYR P  83 
 PHE   0.022   0.001   PHE Q  78 
 HIS   0.011   0.001   HIS O  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (12957)
  covalent geometry    : angle       0.65665 (18797)
  hydrogen bonds       : bond        0.04760 (  628)
  hydrogen bonds       : angle       2.96268 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  120 MET cc_start: 0.7894 (mtp) cc_final: 0.7654 (mtp)
REVERT: N   88 TYR cc_start: 0.7842 (m-80) cc_final: 0.7524 (m-80)
REVERT: P   40 TYR cc_start: 0.8591 (m-80) cc_final: 0.8360 (m-80)
REVERT: Q   73 GLU cc_start: 0.7532 (tt0) cc_final: 0.7143 (tt0)
REVERT: Q   86 SER cc_start: 0.9030 (m) cc_final: 0.8793 (m)
REVERT: Q   94 GLU cc_start: 0.7873 (tp30) cc_final: 0.7445 (tp30)
REVERT: Q  129 ARG cc_start: 0.8040 (ttt-90) cc_final: 0.7617 (mtp-110)
REVERT: S   24 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8210 (mm-40)
REVERT: S  113 LYS cc_start: 0.8088 (tppt) cc_final: 0.7473 (tmtt)
REVERT: T   87 SER cc_start: 0.8523 (m) cc_final: 0.8062 (p)
REVERT: T   93 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7409 (mt-10)
REVERT: T  119 THR cc_start: 0.9162 (t) cc_final: 0.8841 (t)
  outliers start: 32
  outliers final: 24
  residues processed: 163
  average time/residue: 0.1238
  time to fit residues: 27.2882
Evaluate side-chains
  155 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   30 THR
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain N residue   82 THR
Chi-restraints excluded: chain O residue   27 VAL
Chi-restraints excluded: chain O residue   80 THR
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   30 THR
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   23 LEU
Chi-restraints excluded: chain S residue   74 LEU
Chi-restraints excluded: chain S residue   85 GLN
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   35 GLU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   54 ILE
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 88 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** N  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  82 HIS
Q 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.145177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102509 restraints weight = 19621.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.105319 restraints weight = 10482.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.107111 restraints weight = 7293.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.108124 restraints weight = 5979.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.108648 restraints weight = 5398.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12957  Z= 0.192
  Angle     :  0.648  10.287  18797  Z= 0.382
  Chirality :  0.038   0.234   2144
  Planarity :  0.005   0.042   1317
  Dihedral  : 30.862 168.874   4160
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.33 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 18.23 %
    Favored  : 77.10 %
  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: -0.82 (0.31), residues: 732
  helix:  0.28 (0.24), residues: 498
  sheet:  None (None), residues: 0
  loop : -2.28 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R  92 
 TYR   0.030   0.002   TYR P  83 
 PHE   0.017   0.001   PHE Q  78 
 HIS   0.006   0.001   HIS S  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (12957)
  covalent geometry    : angle       0.64771 (18797)
  hydrogen bonds       : bond        0.04767 (  628)
  hydrogen bonds       : angle       2.94115 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   52 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8210 (ttm-80)
REVERT: M  120 MET cc_start: 0.7914 (mtp) cc_final: 0.7681 (mtp)
REVERT: N   88 TYR cc_start: 0.7920 (m-80) cc_final: 0.7672 (m-80)
REVERT: O   88 ILE cc_start: 0.7202 (mt) cc_final: 0.6975 (mm)
REVERT: P  113 GLU cc_start: 0.8563 (tp30) cc_final: 0.8275 (tp30)
REVERT: Q   73 GLU cc_start: 0.7512 (tt0) cc_final: 0.7125 (tt0)
REVERT: Q   86 SER cc_start: 0.9061 (m) cc_final: 0.8791 (m)
REVERT: Q   94 GLU cc_start: 0.7934 (tp30) cc_final: 0.7455 (tp30)
REVERT: Q  129 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7696 (mtp-110)
REVERT: T   86 ARG cc_start: 0.8335 (tpp80) cc_final: 0.8058 (ttm-80)
REVERT: T   87 SER cc_start: 0.8555 (m) cc_final: 0.8059 (p)
REVERT: T   93 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7407 (mt-10)
REVERT: T  119 THR cc_start: 0.9192 (t) cc_final: 0.8889 (t)
  outliers start: 29
  outliers final: 25
  residues processed: 158
  average time/residue: 0.1377
  time to fit residues: 29.4782
Evaluate side-chains
  156 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   30 THR
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain N residue   82 THR
Chi-restraints excluded: chain O residue   27 VAL
Chi-restraints excluded: chain O residue   80 THR
Chi-restraints excluded: chain P residue   56 SER
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   89 ILE
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   30 THR
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   12 THR
Chi-restraints excluded: chain S residue   64 LEU
Chi-restraints excluded: chain S residue   85 GLN
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   35 GLU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0970
   chunk 10 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
P  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.154896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.113118 restraints weight = 21280.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.116200 restraints weight = 11358.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.118093 restraints weight = 7919.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.119124 restraints weight = 6519.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.119777 restraints weight = 5900.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12957  Z= 0.171
  Angle     :  0.624  10.718  18797  Z= 0.369
  Chirality :  0.037   0.203   2144
  Planarity :  0.004   0.043   1317
  Dihedral  : 30.691 170.212   4160
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.64 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 20.16 %
    Favored  : 75.97 %
  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: -0.58 (0.31), residues: 732
  helix:  0.50 (0.24), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.28 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R  92 
 TYR   0.024   0.002   TYR P  83 
 PHE   0.013   0.001   PHE Q  78 
 HIS   0.005   0.001   HIS T  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (12957)
  covalent geometry    : angle       0.62432 (18797)
  hydrogen bonds       : bond        0.04356 (  628)
  hydrogen bonds       : angle       2.80003 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   52 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8190 (ttm-80)
REVERT: P   87 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8181 (p)
REVERT: P  113 GLU cc_start: 0.8483 (tp30) cc_final: 0.8203 (tp30)
REVERT: Q   73 GLU cc_start: 0.7444 (tt0) cc_final: 0.7092 (tt0)
REVERT: Q   86 SER cc_start: 0.9035 (m) cc_final: 0.8800 (m)
REVERT: Q   94 GLU cc_start: 0.7890 (tp30) cc_final: 0.7433 (tp30)
REVERT: Q  129 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7753 (mtp-110)
REVERT: T   86 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7986 (ttm-80)
REVERT: T   87 SER cc_start: 0.8378 (m) cc_final: 0.8025 (p)
REVERT: T   93 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7344 (mt-10)
REVERT: T  120 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8379 (ttpt)
  outliers start: 24
  outliers final: 15
  residues processed: 155
  average time/residue: 0.1410
  time to fit residues: 28.9455
Evaluate side-chains
  148 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain N residue   30 THR
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain O residue   27 VAL
Chi-restraints excluded: chain O residue   80 THR
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   30 THR
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   41 HIS
Chi-restraints excluded: chain T residue   35 GLU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
O  83 HIS
P  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.142533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.099798 restraints weight = 19613.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.102401 restraints weight = 11096.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.103967 restraints weight = 8092.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.104584 restraints weight = 6190.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.104793 restraints weight = 6304.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  12957  Z= 0.269
  Angle     :  0.717  11.042  18797  Z= 0.417
  Chirality :  0.041   0.200   2144
  Planarity :  0.005   0.037   1317
  Dihedral  : 31.040 170.111   4160
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.46 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 20.16 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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 (0.31), residues: 732
  helix:  0.23 (0.24), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.34 (0.35), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R  92 
 TYR   0.034   0.003   TYR P  83 
 PHE   0.013   0.001   PHE Q  78 
 HIS   0.005   0.001   HIS P  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 (12957)
  covalent geometry    : angle       0.71696 (18797)
  hydrogen bonds       : bond        0.06017 (  628)
  hydrogen bonds       : angle       3.33477 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   52 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8291 (ttm-80)
REVERT: M   94 GLU cc_start: 0.8011 (tp30) cc_final: 0.7713 (tp30)
REVERT: P   76 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: Q   73 GLU cc_start: 0.7544 (tt0) cc_final: 0.7172 (tt0)
REVERT: Q   86 SER cc_start: 0.8974 (m) cc_final: 0.8635 (m)
REVERT: Q   94 GLU cc_start: 0.8062 (tp30) cc_final: 0.7559 (tp30)
REVERT: Q  129 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7723 (mtp-110)
REVERT: S   62 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8920 (tm-30)
REVERT: T   87 SER cc_start: 0.8617 (m) cc_final: 0.8130 (p)
REVERT: T   93 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7352 (mt-10)
REVERT: T  116 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7766 (ptpt)
REVERT: T  120 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8367 (ttpp)
  outliers start: 31
  outliers final: 27
  residues processed: 161
  average time/residue: 0.1271
  time to fit residues: 27.7568
Evaluate side-chains
  162 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   30 THR
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain N residue   82 THR
Chi-restraints excluded: chain O residue   27 VAL
Chi-restraints excluded: chain P residue   56 SER
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  115 THR
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain Q residue  109 LEU
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   30 THR
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   12 THR
Chi-restraints excluded: chain S residue   23 LEU
Chi-restraints excluded: chain S residue   41 HIS
Chi-restraints excluded: chain S residue   64 LEU
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Chi-restraints excluded: chain T residue  122 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
M  93 GLN
O  83 HIS
P  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.144794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102230 restraints weight = 19502.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.105010 restraints weight = 10914.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.106428 restraints weight = 8015.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.107466 restraints weight = 6107.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107649 restraints weight = 6034.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.4409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12957  Z= 0.216
  Angle     :  0.667  11.831  18797  Z= 0.391
  Chirality :  0.038   0.170   2144
  Planarity :  0.005   0.041   1317
  Dihedral  : 30.872 170.718   4160
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.64 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 21.13 %
    Favored  : 73.87 %
  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: -0.82 (0.31), residues: 732
  helix:  0.35 (0.24), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.38 (0.35), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R  92 
 TYR   0.059   0.003   TYR N  88 
 PHE   0.010   0.001   PHE M  67 
 HIS   0.005   0.001   HIS P  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (12957)
  covalent geometry    : angle       0.66659 (18797)
  hydrogen bonds       : bond        0.05163 (  628)
  hydrogen bonds       : angle       3.10808 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   52 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8285 (ttm-80)
REVERT: O   88 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7408 (mm)
REVERT: P   76 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7658 (tm-30)
REVERT: P  113 GLU cc_start: 0.8538 (tp30) cc_final: 0.8205 (tp30)
REVERT: Q   73 GLU cc_start: 0.7610 (tt0) cc_final: 0.7167 (tt0)
REVERT: Q   86 SER cc_start: 0.9016 (m) cc_final: 0.8700 (m)
REVERT: Q   94 GLU cc_start: 0.8038 (tp30) cc_final: 0.7501 (tp30)
REVERT: Q  129 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7720 (mtp-110)
REVERT: S   62 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8888 (tm-30)
REVERT: T   86 ARG cc_start: 0.8395 (tpp80) cc_final: 0.8091 (ttm-80)
REVERT: T   87 SER cc_start: 0.8598 (m) cc_final: 0.8074 (p)
REVERT: T   93 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7317 (mt-10)
REVERT: T  120 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8295 (ttpp)
  outliers start: 31
  outliers final: 26
  residues processed: 155
  average time/residue: 0.1292
  time to fit residues: 26.8057
Evaluate side-chains
  153 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   30 THR
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain N residue   82 THR
Chi-restraints excluded: chain O residue   27 VAL
Chi-restraints excluded: chain O residue   88 ILE
Chi-restraints excluded: chain P residue   56 SER
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   30 THR
Chi-restraints excluded: chain R residue   60 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   12 THR
Chi-restraints excluded: chain S residue   23 LEU
Chi-restraints excluded: chain S residue   41 HIS
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   35 GLU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Chi-restraints excluded: chain T residue  122 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
O  83 HIS
P  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.139752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.096929 restraints weight = 19673.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.099391 restraints weight = 11161.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.100955 restraints weight = 8049.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101864 restraints weight = 6732.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.102355 restraints weight = 6127.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.062  12957  Z= 0.344
  Angle     :  0.782  12.076  18797  Z= 0.449
  Chirality :  0.045   0.233   2144
  Planarity :  0.006   0.042   1317
  Dihedral  : 31.267 170.320   4160
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.28 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 20.16 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -1.27 (0.30), residues: 732
  helix: -0.02 (0.23), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.49 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R  92 
 TYR   0.072   0.004   TYR N  88 
 PHE   0.010   0.002   PHE Q  78 
 HIS   0.009   0.002   HIS P  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00801 (12957)
  covalent geometry    : angle       0.78186 (18797)
  hydrogen bonds       : bond        0.06673 (  628)
  hydrogen bonds       : angle       3.62989 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   52 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8300 (ttm-80)
REVERT: M   87 SER cc_start: 0.8999 (t) cc_final: 0.8634 (t)
REVERT: M   94 GLU cc_start: 0.7997 (tp30) cc_final: 0.7749 (tp30)
REVERT: M  120 MET cc_start: 0.7944 (mtp) cc_final: 0.7647 (mtp)
REVERT: O   88 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7708 (mm)
REVERT: P  113 GLU cc_start: 0.8568 (tp30) cc_final: 0.8272 (tp30)
REVERT: Q   73 GLU cc_start: 0.7571 (tt0) cc_final: 0.7162 (tt0)
REVERT: Q   86 SER cc_start: 0.8987 (m) cc_final: 0.8641 (m)
REVERT: Q   94 GLU cc_start: 0.8182 (tp30) cc_final: 0.7676 (tp30)
REVERT: Q  129 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7741 (mtp-110)
REVERT: T   85 LYS cc_start: 0.9140 (pttt) cc_final: 0.8926 (pttm)
REVERT: T   86 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8212 (ttm-80)
REVERT: T   93 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7415 (mt-10)
  outliers start: 36
  outliers final: 27
  residues processed: 164
  average time/residue: 0.1382
  time to fit residues: 30.4842
Evaluate side-chains
  159 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   86 SER
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain N residue   82 THR
Chi-restraints excluded: chain O residue   27 VAL
Chi-restraints excluded: chain O residue   88 ILE
Chi-restraints excluded: chain P residue   52 THR
Chi-restraints excluded: chain P residue   56 SER
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  112 SER
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain P residue  122 THR
Chi-restraints excluded: chain Q residue  109 LEU
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   30 THR
Chi-restraints excluded: chain R residue   60 VAL
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   12 THR
Chi-restraints excluded: chain S residue   23 LEU
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   35 GLU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Chi-restraints excluded: chain T residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
O  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.146013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103900 restraints weight = 19589.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.106629 restraints weight = 10633.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.108348 restraints weight = 7433.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.109341 restraints weight = 6133.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.109909 restraints weight = 5543.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.4738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12957  Z= 0.176
  Angle     :  0.650  12.640  18797  Z= 0.381
  Chirality :  0.037   0.252   2144
  Planarity :  0.004   0.044   1317
  Dihedral  : 30.704 171.537   4160
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.23 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.10 %
    Favored  : 74.03 %
  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: -0.80 (0.31), residues: 732
  helix:  0.36 (0.24), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.42 (0.35), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R  92 
 TYR   0.061   0.003   TYR N  88 
 PHE   0.009   0.001   PHE Q  78 
 HIS   0.003   0.001   HIS P  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (12957)
  covalent geometry    : angle       0.64970 (18797)
  hydrogen bonds       : bond        0.04605 (  628)
  hydrogen bonds       : angle       2.98688 ( 1528)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: M   52 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8264 (ttm-80)
REVERT: M   81 ASP cc_start: 0.8347 (m-30) cc_final: 0.8143 (t0)
REVERT: M   87 SER cc_start: 0.8834 (t) cc_final: 0.8543 (t)
REVERT: M   94 GLU cc_start: 0.8064 (tp30) cc_final: 0.7701 (tp30)
REVERT: P   76 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7658 (tm-30)
REVERT: P  113 GLU cc_start: 0.8566 (tp30) cc_final: 0.8264 (tp30)
REVERT: Q   73 GLU cc_start: 0.7566 (tt0) cc_final: 0.7149 (tt0)
REVERT: Q   86 SER cc_start: 0.8944 (m) cc_final: 0.8705 (m)
REVERT: Q   94 GLU cc_start: 0.7956 (tp30) cc_final: 0.7409 (tp30)
REVERT: Q  129 ARG cc_start: 0.8204 (ttt-90) cc_final: 0.7793 (mtp-110)
REVERT: T   57 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8597 (mttp)
REVERT: T   86 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7993 (ttm-80)
REVERT: T   87 SER cc_start: 0.8625 (m) cc_final: 0.8072 (p)
REVERT: T   93 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7176 (mt-10)
  outliers start: 24
  outliers final: 22
  residues processed: 151
  average time/residue: 0.1295
  time to fit residues: 26.1862
Evaluate side-chains
  148 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   96 CYS
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   62 LEU
Chi-restraints excluded: chain N residue   82 THR
Chi-restraints excluded: chain O residue   27 VAL
Chi-restraints excluded: chain P residue   52 THR
Chi-restraints excluded: chain P residue   56 SER
Chi-restraints excluded: chain P residue   87 SER
Chi-restraints excluded: chain P residue   98 VAL
Chi-restraints excluded: chain P residue  112 SER
Chi-restraints excluded: chain P residue  118 VAL
Chi-restraints excluded: chain P residue  119 THR
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   30 THR
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain S residue   23 LEU
Chi-restraints excluded: chain S residue   41 HIS
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  111 ILE
Chi-restraints excluded: chain T residue   35 GLU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   93 GLU
Chi-restraints excluded: chain T residue   94 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.4980
   chunk 57 optimal weight:    0.3980
   chunk 76 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0570
   chunk 38 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
P  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.148579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.106849 restraints weight = 19548.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.109618 restraints weight = 10482.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.111405 restraints weight = 7295.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.112378 restraints weight = 5983.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.112972 restraints weight = 5418.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12957  Z= 0.168
  Angle     :  0.648  11.525  18797  Z= 0.377
  Chirality :  0.037   0.325   2144
  Planarity :  0.004   0.039   1317
  Dihedral  : 30.607 172.498   4160
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.64 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.90 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.56 (0.31), residues: 732
  helix:  0.57 (0.24), residues: 496
  sheet:  None (None), residues: 0
  loop : -2.44 (0.35), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG S  78 
 TYR   0.067   0.002   TYR N  88 
 PHE   0.007   0.001   PHE Q  78 
 HIS   0.006   0.001   HIS P  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12957)
  covalent geometry    : angle       0.64798 (18797)
  hydrogen bonds       : bond        0.04491 (  628)
  hydrogen bonds       : angle       2.91725 ( 1528)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1856.43 seconds
wall clock time: 32 minutes 40.43 seconds (1960.43 seconds total)