Starting phenix.real_space_refine
on Thu Aug  6 07:38:43 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sn3_40611/08_2026/8sn3_40611.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8276      2.51       5
     N    2716      2.21       5
     O    3291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14612
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 704
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 6, 'TRANS': 80}
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 601
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12313  SG  CYS K  31      31.696  74.358  48.206  1.00 55.65           S
  ATOM  12463  SG  CYS K  51      30.684  71.325  47.252  1.00 54.45           S
  ATOM  12487  SG  CYS K  54      31.262  73.831  44.365  1.00 65.71           S
  ATOM  12204  SG  CYS K  16      21.823  68.573  53.938  1.00 64.66           S
  ATOM  12222  SG  CYS K  19      19.688  65.906  55.446  1.00 64.84           S
  ATOM  12352  SG  CYS K  36      22.524  67.475  57.565  1.00 50.00           S
  ATOM  12374  SG  CYS K  39      23.418  65.177  54.865  1.00 54.15           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  76 " occ=0.25
  Time building chain proxies: 3.39, per 1000 atoms: 0.23
  Number of scatterers: 14612
  At special positions: 0
  Unit cell: (108.896, 134.128, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      33     16.00
     P     294     15.00
     O    3291      8.00
     N    2716      7.00
     C    8276      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 481.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 6


  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 11 sheets defined
      63.1% alpha, 4.5% beta
      135 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.659A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.773A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.748A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.523A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.713A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 122
      removed outlier: 3.714A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.513A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.649A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.505A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.002A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 74
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.534A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.527A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.673A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.837A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.774A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 4.669A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.861A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 90
      removed outlier: 3.792A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.710A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.549A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.564A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.900A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 41
    Processing helix  chain 'M' and resid 55 through 60
      removed outlier: 3.863A  pdb=" N   TYR M  59 " --> pdb=" O   THR M  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.873A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 8.120A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.878A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24
      removed outlier: 4.097A  pdb=" N   SER L  22 " --> pdb=" O   THR L  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15
      removed outlier: 3.627A  pdb=" N   ILE M  13 " --> pdb=" O   VAL M   5 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU M  69 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   HIS M  68 " --> pdb=" O   ILE M  44 " (cutoff:3.500A)

    493 hydrogen bonds defined for protein.
    1447 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      236 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 1.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3244
        1.33 -     1.45: 4467
        1.45 -     1.57: 7137
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15483
  Sorted by residual:
  bond pdb=" C3'  DA J -68 "
       pdb=" C2'  DA J -68 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.36e+01
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.27e+01
  bond pdb=" C3'  DG I -41 "
       pdb=" C2'  DG I -41 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.14e+01
  bond pdb=" C3'  DT J -17 "
       pdb=" C2'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.02e+01
  ... (remaining 15478 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 20752
        1.43 -     2.85: 1345
        2.85 -     4.28: 59
        4.28 -     5.70: 22
        5.70 -     7.13: 4
  Bond angle restraints: 22182
  Sorted by residual:
  angle pdb=" N3   DT J   9 "
        pdb=" C4   DT J   9 "
        pdb=" O4   DT J   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.65   -2.75 6.00e-01 2.78e+00 2.11e+01
  angle pdb=" O4'  DG I  47 "
        pdb=" C4'  DG I  47 "
        pdb=" C3'  DG I  47 "
      ideal   model   delta    sigma   weight residual
     106.00  103.34    2.66 6.00e-01 2.78e+00 1.97e+01
  angle pdb=" N3   DT I   1 "
        pdb=" C4   DT I   1 "
        pdb=" O4   DT I   1 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.93e+01
  angle pdb=" O4'  DA I -35 "
        pdb=" C4'  DA I -35 "
        pdb=" C3'  DA I -35 "
      ideal   model   delta    sigma   weight residual
     106.00  103.38    2.62 6.00e-01 2.78e+00 1.90e+01
  angle pdb=" N3   DT I -65 "
        pdb=" C4   DT I -65 "
        pdb=" O4   DT I -65 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  ... (remaining 22177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 7303
       35.74 -    71.48: 1294
       71.48 -   107.22: 18
      107.22 -   142.96: 0
      142.96 -   178.70: 2
  Dihedral angle restraints: 8617
    sinusoidal: 5475
      harmonic: 3142
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.70 -178.70     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  GLN M  41 "
           pdb=" C   GLN M  41 "
           pdb=" N   ARG M  42 "
           pdb=" CA  ARG M  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.70   19.30     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.33  145.67     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 8614 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1358
       0.029 -    0.059: 740
       0.059 -    0.088: 258
       0.088 -    0.117: 145
       0.117 -    0.146: 15
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CA  ASN G  38 "
            pdb=" N   ASN G  38 "
            pdb=" C   ASN G  38 "
            pdb=" CB  ASN G  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE M  36 "
            pdb=" N   ILE M  36 "
            pdb=" C   ILE M  36 "
            pdb=" CB  ILE M  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1797
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  88 "   -0.019 2.00e-02 2.50e+03   1.74e-02 6.06e+00
        pdb=" CG  TYR F  88 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  88 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  88 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  88 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  88 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F  88 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO M  37 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO M  38 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO M  38 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO M  38 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  88 "    0.010 2.00e-02 2.50e+03   1.33e-02 3.53e+00
        pdb=" CG  TYR B  88 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  88 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  88 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  88 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  88 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  88 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  88 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1794 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 670
        2.71 -     3.26: 13349
        3.26 -     3.81: 26655
        3.81 -     4.35: 31370
        4.35 -     4.90: 46862
  Nonbonded interactions: 118906
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.164 2.496
  nonbonded pdb=" O   ARG L 139 "
            pdb=" NE2 GLN L 143 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR D  40 "
            pdb=" OP1  DG J  48 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NE2 GLN M  31 "
            pdb=" O   ILE M  36 "
     model   vdw
     2.291 3.120
  ... (remaining 118901 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 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:             1.430
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.750
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  15492  Z= 0.477
  Angle     :  0.706   7.129  22194  Z= 0.607
  Chirality :  0.043   0.146   2516
  Planarity :  0.004   0.075   1795
  Dihedral  : 25.549 178.698   6581
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.98 (0.26), residues: 1058
  helix:  2.28 (0.21), residues: 634
  sheet:  1.13 (0.76), residues: 46
  loop : -0.36 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M  74 
 TYR   0.043   0.002   TYR F  88 
 PHE   0.008   0.001   PHE K  53 
 TRP   0.021   0.002   TRP L  33 
 HIS   0.002   0.000   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00541 /  0.48 (15483)
  covalent geometry    : angle       0.70386 /  0.61 (22182)
  hydrogen bonds       : bond        0.11169 /  7.51 (  840)
  hydrogen bonds       : angle       4.09895 /  2.91 ( 2137)
  metal coordination   : bond        0.00134 /  0.07 (    7)
  metal coordination   : angle       3.36711 /  1.64 (    6)
  link_TRANS           : bond        0.00037 /  0.02 (    2)
  link_TRANS           : angle       0.15453 /  0.07 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8701 (tttm)
REVERT: D   68 ASP cc_start: 0.8310 (t70) cc_final: 0.7858 (t0)
REVERT: G   36 LYS cc_start: 0.8763 (mptt) cc_final: 0.8417 (mmtm)
REVERT: H  120 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9041 (ttmt)
REVERT: K   41 GLN cc_start: 0.8920 (tp40) cc_final: 0.8709 (tp40)
REVERT: K   68 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6713 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1367
  time to fit residues: 41.7810
Evaluate side-chains
  182 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:   30.0000
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
** L  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.104866 restraints weight = 32883.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.110650 restraints weight = 62417.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.109869 restraints weight = 25106.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.110570 restraints weight = 20742.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111251 restraints weight = 17171.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (12 function evaluations)
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15492  Z= 0.194
  Angle     :  0.659   9.908  22194  Z= 0.380
  Chirality :  0.043   0.220   2516
  Planarity :  0.005   0.046   1795
  Dihedral  : 28.972 176.850   4412
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.14 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.80 (0.26), residues: 1058
  helix:  2.16 (0.21), residues: 652
  sheet:  1.06 (0.85), residues: 41
  loop : -0.58 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG L 139 
 TYR   0.037   0.002   TYR H  83 
 PHE   0.010   0.001   PHE D  65 
 TRP   0.018   0.004   TRP K  77 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.19 (15483)
  covalent geometry    : angle       0.65624 /  0.38 (22182)
  hydrogen bonds       : bond        0.05947 /  4.03 (  840)
  hydrogen bonds       : angle       3.68729 /  2.65 ( 2137)
  metal coordination   : bond        0.00374 /  0.20 (    7)
  metal coordination   : angle       3.93159 /  1.80 (    6)
  link_TRANS           : bond        0.00019 /  0.01 (    2)
  link_TRANS           : angle       0.22723 /  0.11 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9087 (mttm) cc_final: 0.8690 (mttp)
REVERT: B   88 TYR cc_start: 0.8476 (m-10) cc_final: 0.8226 (m-10)
REVERT: C   95 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8690 (tttm)
REVERT: D   68 ASP cc_start: 0.8387 (t70) cc_final: 0.7883 (t0)
REVERT: D   83 TYR cc_start: 0.8052 (m-10) cc_final: 0.7708 (m-10)
REVERT: G   13 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7682 (ttmm)
REVERT: G   36 LYS cc_start: 0.8907 (mptt) cc_final: 0.8473 (mttm)
REVERT: H   42 TYR cc_start: 0.8640 (t80) cc_final: 0.8238 (t80)
REVERT: H   57 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7586 (mmmm)
REVERT: H  120 LYS cc_start: 0.9199 (ttpt) cc_final: 0.8932 (ttpt)
REVERT: L    9 GLU cc_start: 0.7110 (tt0) cc_final: 0.6771 (tt0)
REVERT: L  147 MET cc_start: 0.4269 (mpp) cc_final: 0.3867 (mpp)
  outliers start: 18
  outliers final: 13
  residues processed: 196
  average time/residue: 0.1320
  time to fit residues: 35.5530
Evaluate side-chains
  188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 102 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9990
   chunk 121 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.146840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.106809 restraints weight = 36737.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.110265 restraints weight = 64586.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.110801 restraints weight = 25043.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.113168 restraints weight = 19177.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113095 restraints weight = 14980.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15492  Z= 0.147
  Angle     :  0.602  11.204  22194  Z= 0.350
  Chirality :  0.040   0.219   2516
  Planarity :  0.004   0.043   1795
  Dihedral  : 29.080 177.786   4412
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.08 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.95 (0.26), residues: 1058
  helix:  2.36 (0.21), residues: 649
  sheet:  0.88 (0.84), residues: 41
  loop : -0.65 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  99 
 TYR   0.018   0.001   TYR H  83 
 PHE   0.023   0.001   PHE L  62 
 TRP   0.021   0.003   TRP L  33 
 HIS   0.002   0.000   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.15 (15483)
  covalent geometry    : angle       0.59889 /  0.35 (22182)
  hydrogen bonds       : bond        0.05215 /  3.54 (  840)
  hydrogen bonds       : angle       3.41982 /  2.47 ( 2137)
  metal coordination   : bond        0.00270 /  0.14 (    7)
  metal coordination   : angle       3.74766 /  1.70 (    6)
  link_TRANS           : bond        0.00069 /  0.03 (    2)
  link_TRANS           : angle       0.18058 /  0.08 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 187
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8518 (m-10) cc_final: 0.8264 (m-10)
REVERT: C   95 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8679 (tttm)
REVERT: D   68 ASP cc_start: 0.8382 (t70) cc_final: 0.8005 (t0)
REVERT: D   83 TYR cc_start: 0.7884 (m-10) cc_final: 0.7483 (m-10)
REVERT: G   36 LYS cc_start: 0.8984 (mptt) cc_final: 0.8560 (mttm)
REVERT: H   42 TYR cc_start: 0.8561 (t80) cc_final: 0.8143 (t80)
REVERT: H  120 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8924 (ttpt)
REVERT: L    5 ARG cc_start: 0.8260 (tpt90) cc_final: 0.7836 (tpt90)
REVERT: L    9 GLU cc_start: 0.7070 (tt0) cc_final: 0.6806 (tt0)
REVERT: L  101 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8540 (mmmm)
REVERT: L  109 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8635 (tt)
REVERT: L  147 MET cc_start: 0.4222 (mpp) cc_final: 0.3658 (mpp)
  outliers start: 18
  outliers final: 11
  residues processed: 197
  average time/residue: 0.1271
  time to fit residues: 34.8455
Evaluate side-chains
  181 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 24 optimal weight:    0.0270
   chunk 101 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 98 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 112 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    1.2044

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.145019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.108403 restraints weight = 36315.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.111594 restraints weight = 76671.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.112441 restraints weight = 30880.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.114839 restraints weight = 22343.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.114914 restraints weight = 15511.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15492  Z= 0.177
  Angle     :  0.625  11.585  22194  Z= 0.354
  Chirality :  0.041   0.227   2516
  Planarity :  0.004   0.044   1795
  Dihedral  : 29.230 177.258   4412
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.95 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.88 (0.26), residues: 1058
  helix:  2.30 (0.21), residues: 649
  sheet:  1.01 (0.83), residues: 41
  loop : -0.68 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  99 
 TYR   0.034   0.002   TYR H  83 
 PHE   0.011   0.001   PHE L  62 
 TRP   0.012   0.002   TRP L  33 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.18 (15483)
  covalent geometry    : angle       0.62177 /  0.35 (22182)
  hydrogen bonds       : bond        0.05474 /  3.71 (  840)
  hydrogen bonds       : angle       3.52719 /  2.55 ( 2137)
  metal coordination   : bond        0.00382 /  0.21 (    7)
  metal coordination   : angle       4.09211 /  1.89 (    6)
  link_TRANS           : bond        0.00032 /  0.02 (    2)
  link_TRANS           : angle       0.24590 /  0.11 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8420 (m-10) cc_final: 0.8013 (m-10)
REVERT: C   95 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8695 (tttm)
REVERT: D   59 MET cc_start: 0.8906 (tpp) cc_final: 0.8699 (tpp)
REVERT: D   68 ASP cc_start: 0.8438 (t70) cc_final: 0.8072 (t0)
REVERT: D   83 TYR cc_start: 0.7946 (m-10) cc_final: 0.7724 (m-10)
REVERT: E  125 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7396 (mt0)
REVERT: F   72 TYR cc_start: 0.8660 (m-80) cc_final: 0.8286 (m-80)
REVERT: G   36 LYS cc_start: 0.8991 (mptt) cc_final: 0.8514 (mttm)
REVERT: H   42 TYR cc_start: 0.8636 (t80) cc_final: 0.8254 (t80)
REVERT: H  120 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8960 (ttpt)
REVERT: K   68 ARG cc_start: 0.7196 (mmp80) cc_final: 0.6761 (ptm160)
REVERT: L    5 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7694 (tpt90)
REVERT: L    9 GLU cc_start: 0.7019 (tt0) cc_final: 0.6583 (tt0)
REVERT: L   69 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6235 (m-10)
REVERT: L  101 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8458 (mmmm)
REVERT: L  147 MET cc_start: 0.4350 (mpp) cc_final: 0.3733 (mpp)
  outliers start: 26
  outliers final: 18
  residues processed: 197
  average time/residue: 0.1299
  time to fit residues: 35.5176
Evaluate side-chains
  194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 174
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain K residue   27 VAL
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 16 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 128 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 86 optimal weight:   20.0000
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.146353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.104103 restraints weight = 33209.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.106734 restraints weight = 56187.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.107886 restraints weight = 29064.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110303 restraints weight = 20240.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110277 restraints weight = 18200.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15492  Z= 0.144
  Angle     :  0.610  13.121  22194  Z= 0.347
  Chirality :  0.040   0.222   2516
  Planarity :  0.004   0.044   1795
  Dihedral  : 29.256 177.731   4412
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.46 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.27), residues: 1058
  helix:  2.41 (0.21), residues: 648
  sheet:  0.97 (0.82), residues: 41
  loop : -0.62 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  99 
 TYR   0.029   0.001   TYR H  83 
 PHE   0.010   0.001   PHE L  62 
 TRP   0.009   0.002   TRP K  61 
 HIS   0.002   0.000   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.14 (15483)
  covalent geometry    : angle       0.60616 /  0.35 (22182)
  hydrogen bonds       : bond        0.05134 /  3.48 (  840)
  hydrogen bonds       : angle       3.40749 /  2.47 ( 2137)
  metal coordination   : bond        0.00349 /  0.20 (    7)
  metal coordination   : angle       4.26082 /  1.96 (    6)
  link_TRANS           : bond        0.00030 /  0.02 (    2)
  link_TRANS           : angle       0.15438 /  0.06 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 185
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8716 (tttm)
REVERT: D   68 ASP cc_start: 0.8371 (t70) cc_final: 0.8011 (t0)
REVERT: E  125 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7263 (mt0)
REVERT: G   36 LYS cc_start: 0.8925 (mptt) cc_final: 0.8487 (mttm)
REVERT: H   42 TYR cc_start: 0.8557 (t80) cc_final: 0.8200 (t80)
REVERT: H  120 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8918 (ttpt)
REVERT: K   77 TRP cc_start: 0.7717 (t-100) cc_final: 0.7389 (t-100)
REVERT: L   69 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6339 (m-10)
REVERT: L  101 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8696 (mmmm)
REVERT: L  109 LEU cc_start: 0.8917 (tt) cc_final: 0.8670 (tt)
REVERT: L  147 MET cc_start: 0.4655 (mpp) cc_final: 0.4056 (mpp)
  outliers start: 23
  outliers final: 16
  residues processed: 197
  average time/residue: 0.1329
  time to fit residues: 36.4288
Evaluate side-chains
  194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 125 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.145916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.089684 restraints weight = 40164.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.091554 restraints weight = 25877.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.091621 restraints weight = 19354.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.091742 restraints weight = 16336.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.091810 restraints weight = 15909.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15492  Z= 0.165
  Angle     :  0.643  13.169  22194  Z= 0.356
  Chirality :  0.042   0.432   2516
  Planarity :  0.005   0.062   1795
  Dihedral  : 29.353 177.396   4412
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.43 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.90 (0.27), residues: 1058
  helix:  2.32 (0.21), residues: 650
  sheet:  1.10 (0.85), residues: 41
  loop : -0.71 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  99 
 TYR   0.037   0.002   TYR H  83 
 PHE   0.032   0.002   PHE L  51 
 TRP   0.017   0.002   TRP L 141 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.17 (15483)
  covalent geometry    : angle       0.63959 /  0.36 (22182)
  hydrogen bonds       : bond        0.05305 /  3.60 (  840)
  hydrogen bonds       : angle       3.47314 /  2.50 ( 2137)
  metal coordination   : bond        0.00341 /  0.18 (    7)
  metal coordination   : angle       4.16060 /  1.96 (    6)
  link_TRANS           : bond        0.00011 /  0.01 (    2)
  link_TRANS           : angle       0.17577 /  0.07 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 188
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9107 (mttm) cc_final: 0.8646 (mttm)
REVERT: C   95 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8819 (tttm)
REVERT: E  125 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7384 (mt0)
REVERT: F   72 TYR cc_start: 0.8780 (m-80) cc_final: 0.8451 (m-80)
REVERT: G   36 LYS cc_start: 0.9015 (mptt) cc_final: 0.8570 (mttm)
REVERT: H   42 TYR cc_start: 0.8584 (t80) cc_final: 0.8166 (t80)
REVERT: H  120 LYS cc_start: 0.9263 (ttpt) cc_final: 0.8857 (ttpt)
REVERT: K   68 ARG cc_start: 0.7548 (mmp80) cc_final: 0.6540 (ptm-80)
REVERT: K   77 TRP cc_start: 0.8154 (t-100) cc_final: 0.7704 (t-100)
REVERT: L    4 LYS cc_start: 0.9072 (mppt) cc_final: 0.8807 (mttp)
REVERT: L    8 LYS cc_start: 0.9314 (mmtt) cc_final: 0.9068 (mmtm)
REVERT: L   93 TRP cc_start: 0.8753 (t-100) cc_final: 0.8518 (t-100)
REVERT: L  101 LYS cc_start: 0.9386 (mmtm) cc_final: 0.9136 (mmmm)
REVERT: L  109 LEU cc_start: 0.9242 (tt) cc_final: 0.9002 (tt)
REVERT: L  147 MET cc_start: 0.6045 (mpp) cc_final: 0.5345 (mpp)
  outliers start: 24
  outliers final: 22
  residues processed: 199
  average time/residue: 0.1452
  time to fit residues: 39.9323
Evaluate side-chains
  205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 128 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 125 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 87 optimal weight:   20.0000
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.145957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.103411 restraints weight = 32913.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.106948 restraints weight = 53193.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.107517 restraints weight = 27315.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.109176 restraints weight = 19348.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.109326 restraints weight = 17728.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15492  Z= 0.149
  Angle     :  0.629  13.079  22194  Z= 0.351
  Chirality :  0.041   0.359   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 29.374 177.693   4412
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.51 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.91 (0.27), residues: 1058
  helix:  2.30 (0.21), residues: 649
  sheet:  1.05 (0.86), residues: 41
  loop : -0.63 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG L 136 
 TYR   0.028   0.002   TYR H  83 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.018   0.002   TRP L  33 
 HIS   0.003   0.000   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 (15483)
  covalent geometry    : angle       0.62509 /  0.35 (22182)
  hydrogen bonds       : bond        0.05140 /  3.48 (  840)
  hydrogen bonds       : angle       3.45386 /  2.49 ( 2137)
  metal coordination   : bond        0.00348 /  0.19 (    7)
  metal coordination   : angle       4.30421 /  2.00 (    6)
  link_TRANS           : bond        0.00027 /  0.01 (    2)
  link_TRANS           : angle       0.11922 /  0.04 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9103 (mttm) cc_final: 0.8677 (mttm)
REVERT: C   95 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8697 (tttm)
REVERT: D   42 TYR cc_start: 0.8546 (t80) cc_final: 0.8332 (t80)
REVERT: E  125 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7298 (mt0)
REVERT: F   72 TYR cc_start: 0.8596 (m-80) cc_final: 0.8276 (m-80)
REVERT: G   36 LYS cc_start: 0.8953 (mptt) cc_final: 0.8501 (mttm)
REVERT: H   42 TYR cc_start: 0.8587 (t80) cc_final: 0.8172 (t80)
REVERT: H  120 LYS cc_start: 0.9224 (ttpt) cc_final: 0.8908 (ttpt)
REVERT: K   61 TRP cc_start: 0.8053 (t60) cc_final: 0.7321 (t60)
REVERT: K   77 TRP cc_start: 0.7861 (t-100) cc_final: 0.7525 (t-100)
REVERT: L   93 TRP cc_start: 0.8407 (t-100) cc_final: 0.8198 (t-100)
REVERT: L  101 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8592 (mmmm)
REVERT: L  109 LEU cc_start: 0.8889 (tt) cc_final: 0.8644 (tt)
REVERT: L  147 MET cc_start: 0.4528 (mpp) cc_final: 0.3876 (mpp)
  outliers start: 26
  outliers final: 21
  residues processed: 196
  average time/residue: 0.1496
  time to fit residues: 40.5568
Evaluate side-chains
  203 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 181
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 117 optimal weight:    0.7980
   chunk 14 optimal weight:    0.1980
   chunk 7 optimal weight:    0.0000
   chunk 55 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    9.9990
   overall best weight:    0.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
L 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.146589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.104267 restraints weight = 33150.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107973 restraints weight = 54815.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108626 restraints weight = 26551.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.109496 restraints weight = 19195.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.109968 restraints weight = 17980.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15492  Z= 0.142
  Angle     :  0.637  13.971  22194  Z= 0.351
  Chirality :  0.041   0.441   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 29.374 177.700   4412
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.84 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.92 (0.27), residues: 1058
  helix:  2.33 (0.21), residues: 650
  sheet:  0.99 (0.85), residues: 41
  loop : -0.68 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG L 136 
 TYR   0.027   0.001   TYR H  83 
 PHE   0.030   0.001   PHE L  51 
 TRP   0.015   0.002   TRP L  33 
 HIS   0.003   0.000   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.14 (15483)
  covalent geometry    : angle       0.63302 /  0.35 (22182)
  hydrogen bonds       : bond        0.04971 /  3.38 (  840)
  hydrogen bonds       : angle       3.43234 /  2.47 ( 2137)
  metal coordination   : bond        0.00314 /  0.18 (    7)
  metal coordination   : angle       4.15383 /  1.94 (    6)
  link_TRANS           : bond        0.00043 /  0.02 (    2)
  link_TRANS           : angle       0.09830 /  0.04 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 182
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8718 (tttm)
REVERT: D   42 TYR cc_start: 0.8567 (t80) cc_final: 0.8347 (t80)
REVERT: D   71 GLU cc_start: 0.7850 (tp30) cc_final: 0.7474 (tp30)
REVERT: E   90 MET cc_start: 0.8602 (mmm) cc_final: 0.8365 (mmm)
REVERT: E  125 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7288 (mt0)
REVERT: G   36 LYS cc_start: 0.8938 (mptt) cc_final: 0.8496 (mttm)
REVERT: H   42 TYR cc_start: 0.8580 (t80) cc_final: 0.8153 (t80)
REVERT: H  120 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8904 (ttpt)
REVERT: K   77 TRP cc_start: 0.7854 (t-100) cc_final: 0.7560 (t-100)
REVERT: L    7 ASN cc_start: 0.8519 (m-40) cc_final: 0.7989 (p0)
REVERT: L  101 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8593 (mmmm)
REVERT: L  109 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8621 (tt)
REVERT: L  147 MET cc_start: 0.4437 (mpp) cc_final: 0.3740 (mpp)
  outliers start: 22
  outliers final: 18
  residues processed: 190
  average time/residue: 0.1414
  time to fit residues: 37.0710
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 87 optimal weight:   20.0000
   chunk 107 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 94 optimal weight:    9.9990
   chunk 109 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
K  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.146027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.091502 restraints weight = 39585.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.091770 restraints weight = 26178.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.091771 restraints weight = 20442.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.092211 restraints weight = 18924.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.092279 restraints weight = 17890.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15492  Z= 0.151
  Angle     :  0.640  14.712  22194  Z= 0.351
  Chirality :  0.041   0.438   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 29.416 177.469   4412
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.49 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.89 (0.27), residues: 1058
  helix:  2.30 (0.21), residues: 650
  sheet:  0.99 (0.85), residues: 41
  loop : -0.67 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 136 
 TYR   0.030   0.002   TYR H  83 
 PHE   0.015   0.001   PHE L  62 
 TRP   0.015   0.002   TRP L  33 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.15 (15483)
  covalent geometry    : angle       0.63600 /  0.35 (22182)
  hydrogen bonds       : bond        0.05075 /  3.44 (  840)
  hydrogen bonds       : angle       3.46169 /  2.49 ( 2137)
  metal coordination   : bond        0.00333 /  0.18 (    7)
  metal coordination   : angle       4.61721 /  2.18 (    6)
  link_TRANS           : bond        0.00024 /  0.01 (    2)
  link_TRANS           : angle       0.11505 /  0.05 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 183
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8811 (tttm)
REVERT: D   42 TYR cc_start: 0.8581 (t80) cc_final: 0.8289 (t80)
REVERT: E  125 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7346 (mt0)
REVERT: F   72 TYR cc_start: 0.8809 (m-80) cc_final: 0.8538 (m-80)
REVERT: G   36 LYS cc_start: 0.9006 (mptt) cc_final: 0.8561 (mttm)
REVERT: H   42 TYR cc_start: 0.8580 (t80) cc_final: 0.8122 (t80)
REVERT: H  120 LYS cc_start: 0.9247 (ttpt) cc_final: 0.8816 (ttpt)
REVERT: K   77 TRP cc_start: 0.8218 (t-100) cc_final: 0.7758 (t-100)
REVERT: L   93 TRP cc_start: 0.8804 (t-100) cc_final: 0.8574 (t-100)
REVERT: L  101 LYS cc_start: 0.9331 (mmtm) cc_final: 0.9017 (mmmm)
REVERT: L  109 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9019 (tt)
REVERT: L  147 MET cc_start: 0.5874 (mpp) cc_final: 0.5067 (mpp)
  outliers start: 22
  outliers final: 20
  residues processed: 190
  average time/residue: 0.1383
  time to fit residues: 36.5504
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 124 optimal weight:    6.9990
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0570
   chunk 27 optimal weight:    5.9990
   chunk 128 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 90 optimal weight:   10.0000
   overall best weight:    0.6702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
L  20 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.146515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.105375 restraints weight = 36764.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111047 restraints weight = 60793.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.110934 restraints weight = 22249.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.111907 restraints weight = 17463.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112096 restraints weight = 15241.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15492  Z= 0.142
  Angle     :  0.636  15.047  22194  Z= 0.350
  Chirality :  0.041   0.453   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 29.409 177.671   4412
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.81 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.88 (0.26), residues: 1058
  helix:  2.29 (0.21), residues: 650
  sheet:  0.90 (0.83), residues: 41
  loop : -0.65 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  99 
 TYR   0.027   0.002   TYR H  83 
 PHE   0.022   0.001   PHE L  51 
 TRP   0.014   0.002   TRP K  61 
 HIS   0.003   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.14 (15483)
  covalent geometry    : angle       0.63190 /  0.35 (22182)
  hydrogen bonds       : bond        0.04972 /  3.38 (  840)
  hydrogen bonds       : angle       3.44314 /  2.48 ( 2137)
  metal coordination   : bond        0.00305 /  0.17 (    7)
  metal coordination   : angle       4.58222 /  2.19 (    6)
  link_TRANS           : bond        0.00028 /  0.01 (    2)
  link_TRANS           : angle       0.07318 /  0.03 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8715 (tttm)
REVERT: D   42 TYR cc_start: 0.8632 (t80) cc_final: 0.8352 (t80)
REVERT: D   71 GLU cc_start: 0.7895 (tp30) cc_final: 0.7473 (tp30)
REVERT: E  125 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7190 (mt0)
REVERT: F   72 TYR cc_start: 0.8665 (m-80) cc_final: 0.8396 (m-80)
REVERT: G   36 LYS cc_start: 0.8961 (mptt) cc_final: 0.8521 (mttm)
REVERT: H   42 TYR cc_start: 0.8591 (t80) cc_final: 0.8153 (t80)
REVERT: H  120 LYS cc_start: 0.9210 (ttpt) cc_final: 0.8875 (ttpt)
REVERT: K   20 MET cc_start: 0.7541 (mmm) cc_final: 0.6625 (mmt)
REVERT: K   61 TRP cc_start: 0.7932 (t60) cc_final: 0.7207 (t60)
REVERT: K   77 TRP cc_start: 0.7850 (t-100) cc_final: 0.7641 (t-100)
REVERT: L    7 ASN cc_start: 0.8614 (m-40) cc_final: 0.8130 (p0)
REVERT: L  101 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8580 (mmmm)
REVERT: L  109 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8582 (tt)
REVERT: L  147 MET cc_start: 0.4695 (mpp) cc_final: 0.4069 (mpp)
  outliers start: 23
  outliers final: 20
  residues processed: 187
  average time/residue: 0.1247
  time to fit residues: 32.8707
Evaluate side-chains
  196 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0870
   chunk 82 optimal weight:    9.9990
   chunk 120 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 99 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 89 optimal weight:   11.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    3.8164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
D  95 GLN
G  89 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.138947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.082664 restraints weight = 38167.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.083170 restraints weight = 26385.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.082907 restraints weight = 20430.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.082971 restraints weight = 20116.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.083079 restraints weight = 19477.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.086  15492  Z= 0.420
  Angle     :  0.910  13.986  22194  Z= 0.472
  Chirality :  0.055   0.411   2516
  Planarity :  0.008   0.086   1795
  Dihedral  : 29.911 175.012   4412
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.24 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  0.52 (0.25), residues: 1058
  helix:  1.14 (0.19), residues: 651
  sheet:  0.79 (0.84), residues: 41
  loop : -1.13 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L 136 
 TYR   0.068   0.004   TYR H  83 
 PHE   0.019   0.003   PHE G  25 
 TRP   0.030   0.004   TRP L  93 
 HIS   0.009   0.002   HIS H  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00989 /  0.42 (15483)
  covalent geometry    : angle       0.90455 /  0.47 (22182)
  hydrogen bonds       : bond        0.08395 /  5.65 (  840)
  hydrogen bonds       : angle       4.31593 /  3.12 ( 2137)
  metal coordination   : bond        0.00711 /  0.32 (    7)
  metal coordination   : angle       6.10079 /  3.08 (    6)
  link_TRANS           : bond        0.00267 /  0.13 (    2)
  link_TRANS           : angle       0.54986 /  0.25 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2256.26 seconds
wall clock time: 39 minutes 32.36 seconds (2372.36 seconds total)