Starting phenix.real_space_refine
on Fri Jul  3 12:49:32 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn3_40611/07_2026/8sn3_40611.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn3_40611/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn3_40611/07_2026/8sn3_40611.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn3_40611/07_2026/8sn3_40611.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn3_40611/07_2026/8sn3_40611.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn3_40611/07_2026/8sn3_40611.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sn3_40611/07_2026/8sn3_40611.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sn3_40611/07_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-dev-6108/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: 3.15, per 1000 atoms: 0.22
  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: 1.16
  Conformation dependent library (CDL) restraints added in 471.5 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: 2.18
  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: 2.41

  Time building geometry restraints manager: 1.56 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: 20764
        1.43 -     2.85: 1334
        2.85 -     4.28: 58
        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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.240
  Find NCS groups from input model:        0.110
  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:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.610
-------------------------------------------------------------------------------
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     :  0.700   7.129  22194  Z= 0.603
  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       0.69840 /  0.60 (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  : 0.386 
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: 0.1427
  time to fit residues: 43.4293
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  : 0.384 
-------------------------------------------------------------------------------
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:   10.0000
   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:   10.0000
   chunk 122 optimal weight:   30.0000
   chunk 91 optimal weight:    9.9990
   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
K  81 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.145512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.104455 restraints weight = 32784.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108293 restraints weight = 62886.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108879 restraints weight = 28376.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.111948 restraints weight = 20321.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.111800 restraints weight = 16381.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    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 = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (12 function evaluations)
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.0973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15492  Z= 0.195
  Angle     :  0.649   9.830  22194  Z= 0.376
  Chirality :  0.042   0.212   2516
  Planarity :  0.005   0.047   1795
  Dihedral  : 29.017 176.488   4412
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.24 %
    Favored  : 86.81 %
  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:  1.05 (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   0.038   0.002   TYR H  83 
 PHE   0.010   0.002   PHE D  65 
 TRP   0.017   0.004   TRP K  77 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.19 (15483)
  covalent geometry    : angle       0.64596 /  0.38 (22182)
  hydrogen bonds       : bond        0.05960 /  4.04 (  840)
  hydrogen bonds       : angle       3.68125 /  2.64 ( 2137)
  metal coordination   : bond        0.00374 /  0.20 (    7)
  metal coordination   : angle       3.92568 /  1.80 (    6)
  link_TRANS           : bond        0.00029 /  0.01 (    2)
  link_TRANS           : angle       0.21263 /  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  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9088 (mttm) cc_final: 0.8696 (mttp)
REVERT: B   88 TYR cc_start: 0.8474 (m-10) cc_final: 0.8235 (m-10)
REVERT: C   95 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8684 (tttm)
REVERT: D   59 MET cc_start: 0.8807 (tpp) cc_final: 0.8544 (tpp)
REVERT: D   68 ASP cc_start: 0.8399 (t70) cc_final: 0.7881 (t0)
REVERT: D   83 TYR cc_start: 0.8071 (m-10) cc_final: 0.7716 (m-10)
REVERT: G   13 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7684 (ttmm)
REVERT: G   36 LYS cc_start: 0.8958 (mptt) cc_final: 0.8521 (mttm)
REVERT: H   42 TYR cc_start: 0.8627 (t80) cc_final: 0.8221 (t80)
REVERT: H   57 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7649 (mmmm)
REVERT: H  120 LYS cc_start: 0.9199 (ttpt) cc_final: 0.8928 (ttpt)
REVERT: L    9 GLU cc_start: 0.7161 (tt0) cc_final: 0.6826 (tt0)
REVERT: L  147 MET cc_start: 0.4331 (mpp) cc_final: 0.3924 (mpp)
  outliers start: 18
  outliers final: 13
  residues processed: 196
  average time/residue: 0.1356
  time to fit residues: 36.1406
Evaluate side-chains
  187 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 102 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 121 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3806 r_free = 0.3806 target = 0.146728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.105669 restraints weight = 36800.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.110779 restraints weight = 59520.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.110761 restraints weight = 22325.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113325 restraints weight = 17508.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.113152 restraints weight = 14137.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1146

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= 0.148
  Angle     :  0.599  10.867  22194  Z= 0.350
  Chirality :  0.040   0.199   2516
  Planarity :  0.004   0.042   1795
  Dihedral  : 29.121 177.267   4412
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.30 %
    Favored  : 84.65 %
  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 (0.26), residues: 1058
  helix:  2.32 (0.21), residues: 649
  sheet:  0.86 (0.83), residues: 41
  loop : -0.65 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 136 
 TYR   0.030   0.001   TYR H  83 
 PHE   0.023   0.001   PHE L  62 
 TRP   0.016   0.002   TRP L  33 
 HIS   0.003   0.000   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.15 (15483)
  covalent geometry    : angle       0.59565 /  0.35 (22182)
  hydrogen bonds       : bond        0.05296 /  3.59 (  840)
  hydrogen bonds       : angle       3.44805 /  2.48 ( 2137)
  metal coordination   : bond        0.00286 /  0.15 (    7)
  metal coordination   : angle       3.89099 /  1.75 (    6)
  link_TRANS           : bond        0.00055 /  0.03 (    2)
  link_TRANS           : angle       0.18454 /  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
  206 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8482 (m-10) cc_final: 0.8231 (m-10)
REVERT: C   95 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8665 (tttm)
REVERT: D   59 MET cc_start: 0.8838 (tpp) cc_final: 0.8594 (tpp)
REVERT: D   68 ASP cc_start: 0.8392 (t70) cc_final: 0.8003 (t0)
REVERT: D   83 TYR cc_start: 0.7904 (m-10) cc_final: 0.7497 (m-10)
REVERT: G   36 LYS cc_start: 0.9021 (mptt) cc_final: 0.8582 (mttm)
REVERT: H   42 TYR cc_start: 0.8584 (t80) cc_final: 0.8153 (t80)
REVERT: H  120 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8905 (ttpt)
REVERT: L    9 GLU cc_start: 0.7263 (tt0) cc_final: 0.6779 (tt0)
REVERT: L  101 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8619 (mmmm)
REVERT: L  147 MET cc_start: 0.4426 (mpp) cc_final: 0.3850 (mpp)
  outliers start: 19
  outliers final: 12
  residues processed: 198
  average time/residue: 0.1427
  time to fit residues: 38.6868
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  : 0.357 
-------------------------------------------------------------------------------
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   72 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 101 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 98 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 112 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0980
   chunk 82 optimal weight:    9.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
M  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.144429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106607 restraints weight = 36415.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.109855 restraints weight = 75332.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110825 restraints weight = 30708.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111748 restraints weight = 23116.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113802 restraints weight = 16981.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15492  Z= 0.206
  Angle     :  0.652  11.953  22194  Z= 0.366
  Chirality :  0.042   0.214   2516
  Planarity :  0.005   0.048   1795
  Dihedral  : 29.353 176.727   4412
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.49 %
    Favored  : 82.59 %
  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:  1.75 (0.26), residues: 1058
  helix:  2.20 (0.21), residues: 649
  sheet:  0.90 (0.82), residues: 41
  loop : -0.73 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L   5 
 TYR   0.018   0.002   TYR H  83 
 PHE   0.012   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        0.00442 /  0.21 (15483)
  covalent geometry    : angle       0.64916 /  0.37 (22182)
  hydrogen bonds       : bond        0.05856 /  3.96 (  840)
  hydrogen bonds       : angle       3.62122 /  2.62 ( 2137)
  metal coordination   : bond        0.00336 /  0.16 (    7)
  metal coordination   : angle       3.98365 /  1.89 (    6)
  link_TRANS           : bond        0.00036 /  0.02 (    2)
  link_TRANS           : angle       0.33127 /  0.15 (    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
  212 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 185
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9051 (mttm) cc_final: 0.8519 (mttp)
REVERT: B   88 TYR cc_start: 0.8454 (m-10) cc_final: 0.8038 (m-10)
REVERT: C   95 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8694 (tttm)
REVERT: D   68 ASP cc_start: 0.8503 (t70) cc_final: 0.8126 (t0)
REVERT: E  125 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7401 (mt0)
REVERT: F   59 LYS cc_start: 0.8338 (tttt) cc_final: 0.8026 (ttpm)
REVERT: F   72 TYR cc_start: 0.8729 (m-80) cc_final: 0.8454 (m-80)
REVERT: G   36 LYS cc_start: 0.8990 (mptt) cc_final: 0.8523 (mttm)
REVERT: H   42 TYR cc_start: 0.8674 (t80) cc_final: 0.8351 (t80)
REVERT: H  120 LYS cc_start: 0.9246 (ttpt) cc_final: 0.8967 (ttpt)
REVERT: L    5 ARG cc_start: 0.7828 (tpt90) cc_final: 0.7319 (tpt90)
REVERT: L    9 GLU cc_start: 0.6857 (tt0) cc_final: 0.6633 (tt0)
REVERT: L   69 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6271 (m-10)
REVERT: L  147 MET cc_start: 0.4431 (mpp) cc_final: 0.3822 (mpp)
  outliers start: 27
  outliers final: 20
  residues processed: 200
  average time/residue: 0.1200
  time to fit residues: 33.4132
Evaluate side-chains
  195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 173
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  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 K residue   27 VAL
Chi-restraints excluded: chain K residue   35 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  143 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 128 optimal weight:   10.0000
   chunk 57 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 112 optimal weight:    7.9990
   chunk 86 optimal weight:   20.0000
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
D  95 GLN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.145905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.105292 restraints weight = 33232.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.111483 restraints weight = 61105.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.110759 restraints weight = 23791.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111463 restraints weight = 19903.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111694 restraints weight = 16409.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    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 = 0.3135 r_free = 0.3135    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: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1483

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= 0.151
  Angle     :  0.617  12.341  22194  Z= 0.353
  Chirality :  0.040   0.206   2516
  Planarity :  0.004   0.041   1795
  Dihedral  : 29.342 177.407   4412
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.11 %
    Favored  : 81.41 %
  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:  1.87 (0.27), residues: 1058
  helix:  2.28 (0.21), residues: 648
  sheet:  0.87 (0.85), residues: 41
  loop : -0.65 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  99 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.016   0.003   TRP L  93 
 HIS   0.006   0.001   HIS L  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.15 (15483)
  covalent geometry    : angle       0.61353 /  0.35 (22182)
  hydrogen bonds       : bond        0.05324 /  3.60 (  840)
  hydrogen bonds       : angle       3.45290 /  2.50 ( 2137)
  metal coordination   : bond        0.00231 /  0.13 (    7)
  metal coordination   : angle       3.84681 /  1.81 (    6)
  link_TRANS           : bond        0.00020 /  0.01 (    2)
  link_TRANS           : angle       0.18203 /  0.07 (    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
  205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8372 (m-10) cc_final: 0.7938 (m-10)
REVERT: C   95 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8712 (tttm)
REVERT: D   68 ASP cc_start: 0.8426 (t70) cc_final: 0.8169 (t0)
REVERT: E  125 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7240 (mt0)
REVERT: F   72 TYR cc_start: 0.8660 (m-80) cc_final: 0.8346 (m-80)
REVERT: G   36 LYS cc_start: 0.8927 (mptt) cc_final: 0.8487 (mttm)
REVERT: H   42 TYR cc_start: 0.8566 (t80) cc_final: 0.8206 (t80)
REVERT: H  120 LYS cc_start: 0.9227 (ttpt) cc_final: 0.8949 (ttpt)
REVERT: K   77 TRP cc_start: 0.7592 (t-100) cc_final: 0.7329 (t-100)
REVERT: L    4 LYS cc_start: 0.8386 (mttp) cc_final: 0.8152 (mtmt)
REVERT: L    7 ASN cc_start: 0.8237 (m110) cc_final: 0.7921 (p0)
REVERT: L   32 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.7030 (m-70)
REVERT: L   69 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6254 (m-10)
REVERT: L  147 MET cc_start: 0.4570 (mpp) cc_final: 0.4000 (mpp)
  outliers start: 23
  outliers final: 14
  residues processed: 196
  average time/residue: 0.1353
  time to fit residues: 36.5391
Evaluate side-chains
  192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
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 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 70 optimal weight:    0.7980
   chunk 125 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
D  95 GLN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.089271 restraints weight = 40319.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.090054 restraints weight = 25691.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.090135 restraints weight = 21594.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.090737 restraints weight = 18695.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.090689 restraints weight = 15889.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    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 = 0.2884 r_free = 0.2884    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 (10 function evaluations)
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.1550

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= 0.145
  Angle     :  0.621  13.171  22194  Z= 0.352
  Chirality :  0.040   0.205   2516
  Planarity :  0.004   0.050   1795
  Dihedral  : 29.376 177.398   4412
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.97 %
    Favored  : 80.54 %
  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 (0.27), residues: 1058
  helix:  2.30 (0.21), residues: 652
  sheet:  1.02 (0.83), residues: 41
  loop : -0.73 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG L 136 
 TYR   0.012   0.001   TYR H  83 
 PHE   0.031   0.001   PHE L  51 
 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        0.00265 /  0.14 (15483)
  covalent geometry    : angle       0.61860 /  0.35 (22182)
  hydrogen bonds       : bond        0.05154 /  3.50 (  840)
  hydrogen bonds       : angle       3.44420 /  2.48 ( 2137)
  metal coordination   : bond        0.00201 /  0.11 (    7)
  metal coordination   : angle       3.69214 /  1.77 (    6)
  link_TRANS           : bond        0.00034 /  0.02 (    2)
  link_TRANS           : angle       0.14659 /  0.05 (    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
  210 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 187
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8403 (pp30) cc_final: 0.8202 (pp30)
REVERT: B   77 LYS cc_start: 0.9113 (mttm) cc_final: 0.8645 (mttm)
REVERT: C   95 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8808 (tttm)
REVERT: D   68 ASP cc_start: 0.8371 (t70) cc_final: 0.8089 (t0)
REVERT: E  125 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7386 (mt0)
REVERT: G   36 LYS cc_start: 0.8968 (mptt) cc_final: 0.8555 (mttm)
REVERT: H   42 TYR cc_start: 0.8553 (t80) cc_final: 0.8136 (t80)
REVERT: H  120 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8829 (ttpt)
REVERT: K   68 ARG cc_start: 0.7259 (mmp80) cc_final: 0.6664 (ptm-80)
REVERT: K   77 TRP cc_start: 0.8183 (t-100) cc_final: 0.7756 (t-100)
REVERT: L  109 LEU cc_start: 0.9243 (tt) cc_final: 0.9020 (tt)
REVERT: L  147 MET cc_start: 0.6359 (mpp) cc_final: 0.5568 (mpp)
  outliers start: 23
  outliers final: 19
  residues processed: 197
  average time/residue: 0.1462
  time to fit residues: 39.9829
Evaluate side-chains
  202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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   13 LYS
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
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:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 103 optimal weight:    0.1980
   chunk 33 optimal weight:    0.7980
   chunk 125 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 87 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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
L  32 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.145864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.103507 restraints weight = 33149.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.109077 restraints weight = 53676.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.108849 restraints weight = 21888.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.109609 restraints weight = 17119.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.109961 restraints weight = 15877.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    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 = 0.3100 r_free = 0.3100    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 (6 function evaluations)
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1614

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= 0.148
  Angle     :  0.618  12.817  22194  Z= 0.349
  Chirality :  0.040   0.206   2516
  Planarity :  0.004   0.047   1795
  Dihedral  : 29.436 177.309   4412
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 7.94
  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:  2.32 (0.21), residues: 649
  sheet:  1.05 (0.85), residues: 41
  loop : -0.66 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 136 
 TYR   0.017   0.001   TYR H  83 
 PHE   0.022   0.001   PHE L  62 
 TRP   0.016   0.002   TRP L  33 
 HIS   0.003   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.15 (15483)
  covalent geometry    : angle       0.61513 /  0.35 (22182)
  hydrogen bonds       : bond        0.05128 /  3.48 (  840)
  hydrogen bonds       : angle       3.45559 /  2.48 ( 2137)
  metal coordination   : bond        0.00240 /  0.12 (    7)
  metal coordination   : angle       3.86848 /  1.85 (    6)
  link_TRANS           : bond        0.00032 /  0.02 (    2)
  link_TRANS           : angle       0.13785 /  0.05 (    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
  209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8443 (pp30) cc_final: 0.8242 (pp30)
REVERT: B   77 LYS cc_start: 0.9110 (mttm) cc_final: 0.8690 (mttm)
REVERT: B   88 TYR cc_start: 0.8474 (m-10) cc_final: 0.8111 (m-10)
REVERT: C   95 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8700 (tttm)
REVERT: D   68 ASP cc_start: 0.8366 (t70) cc_final: 0.8076 (t0)
REVERT: E  125 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7235 (mt0)
REVERT: F   72 TYR cc_start: 0.8604 (m-80) cc_final: 0.8230 (m-80)
REVERT: G   36 LYS cc_start: 0.8949 (mptt) cc_final: 0.8495 (mttm)
REVERT: H   42 TYR cc_start: 0.8601 (t80) cc_final: 0.8179 (t80)
REVERT: H  120 LYS cc_start: 0.9230 (ttpt) cc_final: 0.8913 (ttpt)
REVERT: K   61 TRP cc_start: 0.8041 (t60) cc_final: 0.7321 (t60)
REVERT: K   77 TRP cc_start: 0.7867 (t-100) cc_final: 0.7562 (t-100)
REVERT: L    9 GLU cc_start: 0.7475 (tt0) cc_final: 0.7257 (tt0)
REVERT: L  109 LEU cc_start: 0.8884 (tt) cc_final: 0.8638 (tt)
REVERT: L  147 MET cc_start: 0.4692 (mpp) cc_final: 0.4005 (mpp)
  outliers start: 26
  outliers final: 21
  residues processed: 195
  average time/residue: 0.1357
  time to fit residues: 36.4967
Evaluate side-chains
  201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue   46 LYS
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:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0980
   chunk 55 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 59 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.145767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.103134 restraints weight = 33212.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.105824 restraints weight = 54972.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.106568 restraints weight = 30175.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.109955 restraints weight = 20811.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109659 restraints weight = 17732.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    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 = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15492  Z= 0.142
  Angle     :  0.621  13.205  22194  Z= 0.349
  Chirality :  0.040   0.213   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 29.437 177.384   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 :  2.27 %
    Allowed  : 18.59 %
    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:  1.90 (0.27), residues: 1058
  helix:  2.31 (0.21), residues: 650
  sheet:  1.24 (0.88), residues: 41
  loop : -0.71 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG L 136 
 TYR   0.010   0.001   TYR H  83 
 PHE   0.031   0.002   PHE L  51 
 TRP   0.012   0.001   TRP L  33 
 HIS   0.003   0.000   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.14 (15483)
  covalent geometry    : angle       0.61791 /  0.35 (22182)
  hydrogen bonds       : bond        0.05001 /  3.40 (  840)
  hydrogen bonds       : angle       3.43302 /  2.47 ( 2137)
  metal coordination   : bond        0.00214 /  0.12 (    7)
  metal coordination   : angle       3.82769 /  1.83 (    6)
  link_TRANS           : bond        0.00038 /  0.02 (    2)
  link_TRANS           : angle       0.10861 /  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: 21
    poor density    : 183
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8511 (m-10) cc_final: 0.8250 (m-10)
REVERT: C   95 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8714 (tttm)
REVERT: D   42 TYR cc_start: 0.8590 (t80) cc_final: 0.8339 (t80)
REVERT: D   68 ASP cc_start: 0.8265 (t70) cc_final: 0.7732 (t0)
REVERT: E   90 MET cc_start: 0.8643 (mmm) cc_final: 0.8411 (mmm)
REVERT: E  125 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7195 (mt0)
REVERT: G   36 LYS cc_start: 0.8954 (mptt) cc_final: 0.8503 (mttm)
REVERT: H   42 TYR cc_start: 0.8581 (t80) cc_final: 0.8144 (t80)
REVERT: H  120 LYS cc_start: 0.9220 (ttpt) cc_final: 0.8905 (ttpt)
REVERT: K   77 TRP cc_start: 0.7872 (t-100) cc_final: 0.7538 (t-100)
REVERT: L    7 ASN cc_start: 0.8745 (m110) cc_final: 0.8240 (p0)
REVERT: L    9 GLU cc_start: 0.7423 (tt0) cc_final: 0.7155 (tt0)
REVERT: L  109 LEU cc_start: 0.8912 (tt) cc_final: 0.8665 (tt)
REVERT: L  147 MET cc_start: 0.4482 (mpp) cc_final: 0.3897 (mpp)
  outliers start: 21
  outliers final: 18
  residues processed: 191
  average time/residue: 0.1562
  time to fit residues: 40.9895
Evaluate side-chains
  195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 176
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
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 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 H residue   46 LYS
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
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:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 94 optimal weight:   10.0000
   chunk 109 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.146012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.090097 restraints weight = 39563.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.090953 restraints weight = 25861.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.090951 restraints weight = 21668.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.091281 restraints weight = 18744.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.091431 restraints weight = 18002.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (11 function evaluations)
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15492  Z= 0.151
  Angle     :  0.641  14.706  22194  Z= 0.355
  Chirality :  0.041   0.335   2516
  Planarity :  0.004   0.036   1795
  Dihedral  : 29.469 177.259   4412
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.14 %
    Favored  : 78.38 %
  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:  1.85 (0.26), residues: 1058
  helix:  2.26 (0.21), residues: 650
  sheet:  1.28 (0.89), residues: 41
  loop : -0.71 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  99 
 TYR   0.014   0.001   TYR H  83 
 PHE   0.032   0.001   PHE L  62 
 TRP   0.012   0.001   TRP K  61 
 HIS   0.004   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 (15483)
  covalent geometry    : angle       0.63749 /  0.35 (22182)
  hydrogen bonds       : bond        0.05079 /  3.45 (  840)
  hydrogen bonds       : angle       3.47604 /  2.49 ( 2137)
  metal coordination   : bond        0.00243 /  0.13 (    7)
  metal coordination   : angle       4.11164 /  1.99 (    6)
  link_TRANS           : bond        0.00029 /  0.01 (    2)
  link_TRANS           : angle       0.12217 /  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: 23
    poor density    : 182
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8526 (m-10) cc_final: 0.8275 (m-10)
REVERT: C   95 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8814 (tttm)
REVERT: D   42 TYR cc_start: 0.8597 (t80) cc_final: 0.8287 (t80)
REVERT: D   68 ASP cc_start: 0.8262 (t70) cc_final: 0.7974 (t0)
REVERT: D   71 GLU cc_start: 0.7950 (tp30) cc_final: 0.7600 (tp30)
REVERT: E  125 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7345 (mt0)
REVERT: F   72 TYR cc_start: 0.8801 (m-80) cc_final: 0.8497 (m-80)
REVERT: G   36 LYS cc_start: 0.8993 (mptt) cc_final: 0.8563 (mttm)
REVERT: H   42 TYR cc_start: 0.8573 (t80) cc_final: 0.8114 (t80)
REVERT: H  120 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8819 (ttpt)
REVERT: K   61 TRP cc_start: 0.7967 (t60) cc_final: 0.7069 (t60)
REVERT: K   77 TRP cc_start: 0.8227 (t-100) cc_final: 0.7755 (t-100)
REVERT: L  109 LEU cc_start: 0.9249 (tt) cc_final: 0.9024 (tt)
REVERT: L  147 MET cc_start: 0.6290 (mpp) cc_final: 0.5503 (mpp)
  outliers start: 23
  outliers final: 19
  residues processed: 191
  average time/residue: 0.1436
  time to fit residues: 37.8844
Evaluate side-chains
  195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 175
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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   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 H residue   46 LYS
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 71 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0370
   chunk 110 optimal weight:    4.9990
   chunk 27 optimal weight:    0.2980
   chunk 128 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 90 optimal weight:   10.0000
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.146764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.105838 restraints weight = 36734.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.111288 restraints weight = 60352.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.111153 restraints weight = 22296.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113027 restraints weight = 17554.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.113061 restraints weight = 14592.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15492  Z= 0.140
  Angle     :  0.638  15.249  22194  Z= 0.355
  Chirality :  0.041   0.257   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 29.453 177.438   4412
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.57 %
    Favored  : 78.16 %
  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 (0.26), residues: 1058
  helix:  2.30 (0.21), residues: 650
  sheet:  1.20 (0.87), residues: 41
  loop : -0.69 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 136 
 TYR   0.021   0.001   TYR H  83 
 PHE   0.033   0.002   PHE L  62 
 TRP   0.012   0.001   TRP K  61 
 HIS   0.004   0.000   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.14 (15483)
  covalent geometry    : angle       0.63452 /  0.35 (22182)
  hydrogen bonds       : bond        0.04926 /  3.34 (  840)
  hydrogen bonds       : angle       3.43530 /  2.46 ( 2137)
  metal coordination   : bond        0.00227 /  0.13 (    7)
  metal coordination   : angle       4.15918 /  2.01 (    6)
  link_TRANS           : bond        0.00043 /  0.02 (    2)
  link_TRANS           : angle       0.06816 /  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
  198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9137 (mttm) cc_final: 0.8577 (mttm)
REVERT: B   88 TYR cc_start: 0.8478 (m-10) cc_final: 0.8268 (m-10)
REVERT: C   95 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8705 (tttm)
REVERT: D   42 TYR cc_start: 0.8650 (t80) cc_final: 0.8349 (t80)
REVERT: D   68 ASP cc_start: 0.8276 (t70) cc_final: 0.7727 (t0)
REVERT: D   71 GLU cc_start: 0.7857 (tp30) cc_final: 0.7484 (tp30)
REVERT: E  125 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7217 (mt0)
REVERT: F   72 TYR cc_start: 0.8612 (m-80) cc_final: 0.8267 (m-80)
REVERT: G   36 LYS cc_start: 0.8960 (mptt) cc_final: 0.8514 (mttm)
REVERT: H   42 TYR cc_start: 0.8583 (t80) cc_final: 0.8149 (t80)
REVERT: H  120 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8888 (ttpt)
REVERT: K   20 MET cc_start: 0.7391 (mmm) cc_final: 0.6555 (mmt)
REVERT: K   61 TRP cc_start: 0.7916 (t60) cc_final: 0.7212 (t60)
REVERT: K   68 ARG cc_start: 0.7556 (mmp80) cc_final: 0.6307 (ptm-80)
REVERT: K   77 TRP cc_start: 0.7867 (t-100) cc_final: 0.7637 (t-100)
REVERT: L    9 GLU cc_start: 0.7126 (tt0) cc_final: 0.6281 (tt0)
REVERT: L  147 MET cc_start: 0.4675 (mpp) cc_final: 0.4012 (mpp)
  outliers start: 21
  outliers final: 19
  residues processed: 185
  average time/residue: 0.1533
  time to fit residues: 39.2549
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  : 0.404 
-------------------------------------------------------------------------------
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   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 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 H residue   46 LYS
Chi-restraints excluded: chain K residue   35 LEU
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=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:    0.0980
   chunk 82 optimal weight:    9.9990
   chunk 120 optimal weight:    0.8980
   chunk 80 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   chunk 75 optimal weight:    9.9990
   overall best weight:    3.1986

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.140057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.083797 restraints weight = 38008.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.083565 restraints weight = 26158.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.083836 restraints weight = 22102.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.083930 restraints weight = 19923.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.084091 restraints weight = 19462.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.077  15492  Z= 0.355
  Angle     :  0.841  14.249  22194  Z= 0.442
  Chirality :  0.051   0.458   2516
  Planarity :  0.007   0.071   1795
  Dihedral  : 29.858 175.893   4412
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.68 %
    Favored  : 77.84 %
  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:  0.91 (0.25), residues: 1058
  helix:  1.48 (0.20), residues: 648
  sheet:  1.13 (0.87), residues: 41
  loop : -1.03 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K  68 
 TYR   0.028   0.003   TYR D  83 
 PHE   0.043   0.003   PHE L  62 
 TRP   0.012   0.002   TRP L  33 
 HIS   0.008   0.002   HIS H  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00833 /  0.35 (15483)
  covalent geometry    : angle       0.83653 /  0.44 (22182)
  hydrogen bonds       : bond        0.07524 /  5.07 (  840)
  hydrogen bonds       : angle       4.13327 /  2.99 ( 2137)
  metal coordination   : bond        0.00552 /  0.26 (    7)
  metal coordination   : angle       5.29578 /  2.70 (    6)
  link_TRANS           : bond        0.00216 /  0.11 (    2)
  link_TRANS           : angle       0.51082 /  0.24 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2367.61 seconds
wall clock time: 41 minutes 28.87 seconds (2488.87 seconds total)