Starting phenix.real_space_refine
on Thu Aug  6 07:50:56 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn5_40613/08_2026/8sn5_40613.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14600
  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: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    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: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          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  12296  SG  CYS K  31      32.772  74.839  47.610  1.00 92.05           S
  ATOM  12446  SG  CYS K  51      33.544  71.534  45.841  1.00 78.30           S
  ATOM  12470  SG  CYS K  54      32.537  74.397  43.794  1.00100.28           S
  ATOM  12187  SG  CYS K  16      22.380  68.849  53.466  1.00109.61           S
  ATOM  12205  SG  CYS K  19      20.326  66.237  55.227  1.00105.23           S
  ATOM  12335  SG  CYS K  36      23.285  67.916  57.089  1.00 94.72           S
  ATOM  12357  SG  CYS K  39      24.037  65.484  54.484  1.00 92.21           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
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.46, per 1000 atoms: 0.24
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (108.896, 134.128, 127.488, 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    3289      8.00
     N    2713      7.00
     C    8269      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: 1.22
  Conformation dependent library (CDL) restraints added in 542.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
      Number of angles added : 9


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 13 sheets defined
      63.6% alpha, 5.3% beta
      135 base pairs and 233 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.502A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.794A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.921A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.776A  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 21
      removed outlier: 4.203A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.476A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.813A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.725A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.708A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.803A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    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 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.571A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.543A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.571A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.619A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.596A  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: 3.702A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.773A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 4.256A  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 39
      No H-bonds generated for 'chain 'M' and resid 37 through 39'
    Processing helix  chain 'M' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.679A  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
      removed outlier: 3.738A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    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: 7.809A  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 'C' and resid 101 through 102
      removed outlier: 6.826A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.004A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.679A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28
      removed outlier: 4.096A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16
      removed outlier: 3.623A  pdb=" N   VAL M   5 " --> pdb=" O   ILE M  13 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LEU M  15 " --> pdb=" O   ILE M   3 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE M   3 " --> pdb=" O   LEU M  15 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   LEU M  67 " --> pdb=" O   GLN M   2 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   PHE M   4 " --> pdb=" O   LEU M  67 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU M  69 " --> pdb=" O   PHE M   4 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LYS M   6 " --> pdb=" O   LEU M  69 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU M  71 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG M  42 " --> pdb=" O   VAL M  70 " (cutoff:3.500A)

    501 hydrogen bonds defined for protein.
    1464 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      233 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3384
        1.34 -     1.45: 4369
        1.45 -     1.57: 7084
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.16e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    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 -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+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 1.07e+01
  bond pdb=" C3'  DG I -41 "
       pdb=" C2'  DG I -41 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 20945
        1.54 -     3.07: 1147
        3.07 -     4.61: 57
        4.61 -     6.14: 16
        6.14 -     7.68: 6
  Bond angle restraints: 22171
  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  122.58   -2.68 6.00e-01 2.78e+00 2.00e+01
  angle pdb=" O4'  DT I -26 "
        pdb=" C4'  DT I -26 "
        pdb=" C3'  DT I -26 "
      ideal   model   delta    sigma   weight residual
     106.00  103.36    2.64 6.00e-01 2.78e+00 1.94e+01
  angle pdb=" N3   DT I -17 "
        pdb=" C4   DT I -17 "
        pdb=" O4   DT I -17 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.89e+01
  angle pdb=" N3   DT J  66 "
        pdb=" C4   DT J  66 "
        pdb=" O4   DT J  66 "
      ideal   model   delta    sigma   weight residual
     119.90  122.49   -2.59 6.00e-01 2.78e+00 1.87e+01
  angle pdb=" N3   DT I -59 "
        pdb=" C4   DT I -59 "
        pdb=" O4   DT I -59 "
      ideal   model   delta    sigma   weight residual
     119.90  122.45   -2.55 6.00e-01 2.78e+00 1.80e+01
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 7298
       35.68 -    71.35: 1294
       71.35 -   107.03: 17
      107.03 -   142.70: 0
      142.70 -   178.38: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  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   38.38 -178.38     1      3.50e+01 8.16e-04 1.57e+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   76.32  143.68     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CA  ARG L 131 "
           pdb=" C   ARG L 131 "
           pdb=" N   ASP L 132 "
           pdb=" CA  ASP L 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.15  -17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1418
       0.031 -    0.061: 706
       0.061 -    0.092: 229
       0.092 -    0.123: 150
       0.123 -    0.153: 13
  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 5.88e-01
  chirality pdb=" CA  GLN A 125 "
            pdb=" N   GLN A 125 "
            pdb=" C   GLN A 125 "
            pdb=" CB  GLN A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.78e-01
  chirality pdb=" CA  GLU K  25 "
            pdb=" N   GLU K  25 "
            pdb=" C   GLU K  25 "
            pdb=" CB  GLU K  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.52e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L 141 "    0.030 2.00e-02 2.50e+03   2.98e-02 2.23e+01
        pdb=" CG  TRP L 141 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD1 TRP L 141 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP L 141 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP L 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP L 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP L 141 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP L 141 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.022 2.00e-02 2.50e+03   9.23e-03 2.34e+00
        pdb=" N9   DA I -35 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -54 "    0.020 2.00e-02 2.50e+03   9.03e-03 2.24e+00
        pdb=" N9   DA I -54 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8   DA I -54 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I -54 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I -54 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -54 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -54 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -54 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I -54 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3   DA I -54 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -54 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 413
        2.68 -     3.24: 13032
        3.24 -     3.79: 26278
        3.79 -     4.35: 32109
        4.35 -     4.90: 47543
  Nonbonded interactions: 119375
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.131 2.496
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER L  91 "
            pdb=" OE1 GLN L  92 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD1 ASP L 130 "
            pdb=" NZ  LYS L 133 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" OE2 GLU A  94 "
            pdb=" NE2 GLN G 104 "
     model   vdw
     2.243 3.120
  ... (remaining 119370 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=0.17 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:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.650
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
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   0.059  15482  Z= 0.473
  Angle     :  0.718   7.753  22186  Z= 0.608
  Chirality :  0.044   0.153   2516
  Planarity :  0.004   0.037   1794
  Dihedral  : 25.638 178.379   6577
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    Favored  : 99.68 %
  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:  2.26 (0.27), residues: 1057
  helix:  2.63 (0.21), residues: 646
  sheet:  0.85 (0.75), residues: 47
  loop : -0.56 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 131 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.006   0.001   PHE D  70 
 TRP   0.081   0.005   TRP L 141 
 HIS   0.005   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00527 /  0.47 (15472)
  covalent geometry    : angle       0.71413 /  0.61 (22171)
  hydrogen bonds       : bond        0.10388 /  6.70 (  848)
  hydrogen bonds       : angle       3.98729 /  2.77 ( 2154)
  metal coordination   : bond        0.02151 /  1.07 (    8)
  metal coordination   : angle       3.91026 /  1.99 (    9)
  link_TRANS           : bond        0.00088 /  0.05 (    2)
  link_TRANS           : angle       0.68680 /  0.29 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9152 (mt) cc_final: 0.8940 (mt)
REVERT: C   39 TYR cc_start: 0.8837 (m-80) cc_final: 0.8517 (m-80)
REVERT: D  108 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8001 (mtmt)
REVERT: H   31 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7416 (mmp80)
REVERT: H   35 GLU cc_start: 0.8641 (mp0) cc_final: 0.8420 (mp0)
REVERT: H   89 ILE cc_start: 0.9224 (mt) cc_final: 0.9005 (mt)
REVERT: K   13 GLU cc_start: 0.8434 (tp30) cc_final: 0.8138 (tm-30)
REVERT: L   60 TYR cc_start: 0.7143 (t80) cc_final: 0.6811 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1543
  time to fit residues: 60.4030
Evaluate side-chains
  225 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   overall best weight:    2.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
F  75 HIS
G  38 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  81 GLN
K  83 HIS
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  46 GLN
M   2 GLN
M  25 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.118325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.081093 restraints weight = 53616.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.082818 restraints weight = 34168.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.082626 restraints weight = 31326.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.082989 restraints weight = 20552.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.083546 restraints weight = 18174.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (14 function evaluations)
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  15482  Z= 0.251
  Angle     :  0.721  10.380  22186  Z= 0.408
  Chirality :  0.046   0.261   2516
  Planarity :  0.005   0.056   1794
  Dihedral  : 29.078 175.853   4413
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.42 %
    Favored  : 84.74 %
  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: 1057
  helix:  2.38 (0.21), residues: 652
  sheet:  0.51 (0.69), residues: 50
  loop : -0.78 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  86 
 TYR   0.025   0.003   TYR L 127 
 PHE   0.014   0.002   PHE K  40 
 TRP   0.058   0.006   TRP L 141 
 HIS   0.008   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00545 /  0.25 (15472)
  covalent geometry    : angle       0.71159 /  0.41 (22171)
  hydrogen bonds       : bond        0.05885 /  3.91 (  848)
  hydrogen bonds       : angle       3.80446 /  2.71 ( 2154)
  metal coordination   : bond        0.01759 /  0.87 (    8)
  metal coordination   : angle       5.75452 /  2.62 (    9)
  link_TRANS           : bond        0.00224 /  0.11 (    2)
  link_TRANS           : angle       0.73300 /  0.28 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 237
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9206 (t) cc_final: 0.8095 (t)
REVERT: A   59 GLU cc_start: 0.8874 (pm20) cc_final: 0.8023 (pm20)
REVERT: A   60 LEU cc_start: 0.9253 (mt) cc_final: 0.8968 (mt)
REVERT: A  125 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7253 (pm20)
REVERT: D  108 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8095 (mtmt)
REVERT: F   88 TYR cc_start: 0.8891 (m-80) cc_final: 0.8510 (m-80)
REVERT: H   35 GLU cc_start: 0.8986 (mp0) cc_final: 0.8664 (mp0)
REVERT: L   60 TYR cc_start: 0.7501 (t80) cc_final: 0.7185 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 245
  average time/residue: 0.1409
  time to fit residues: 48.6138
Evaluate side-chains
  220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 208
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain L residue   55 HIS
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 100 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 101 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 102 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  81 GLN
L   7 ASN
L  34 GLN
M  25 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.119395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.080720 restraints weight = 47210.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.080461 restraints weight = 28585.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.080793 restraints weight = 29282.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.081292 restraints weight = 20975.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.082245 restraints weight = 18294.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15482  Z= 0.159
  Angle     :  0.667  11.765  22186  Z= 0.380
  Chirality :  0.043   0.259   2516
  Planarity :  0.004   0.062   1794
  Dihedral  : 29.152 176.950   4413
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.91 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.27), residues: 1057
  helix:  2.46 (0.21), residues: 651
  sheet:  0.07 (0.67), residues: 50
  loop : -0.77 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 139 
 TYR   0.034   0.002   TYR L 145 
 PHE   0.014   0.001   PHE M  45 
 TRP   0.053   0.004   TRP L 141 
 HIS   0.004   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.16 (15472)
  covalent geometry    : angle       0.65703 /  0.38 (22171)
  hydrogen bonds       : bond        0.05158 /  3.41 (  848)
  hydrogen bonds       : angle       3.46191 /  2.47 ( 2154)
  metal coordination   : bond        0.01468 /  0.73 (    8)
  metal coordination   : angle       5.63106 /  2.47 (    9)
  link_TRANS           : bond        0.00099 /  0.05 (    2)
  link_TRANS           : angle       0.29545 /  0.14 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 226
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9171 (t) cc_final: 0.8033 (t)
REVERT: A   59 GLU cc_start: 0.8909 (pm20) cc_final: 0.8162 (pm20)
REVERT: A   60 LEU cc_start: 0.9166 (mt) cc_final: 0.8953 (mt)
REVERT: A  125 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7254 (pm20)
REVERT: C  110 ASN cc_start: 0.8578 (p0) cc_final: 0.8348 (p0)
REVERT: D  108 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8107 (mtpt)
REVERT: F   88 TYR cc_start: 0.8922 (m-80) cc_final: 0.8597 (m-80)
REVERT: H   35 GLU cc_start: 0.8977 (mp0) cc_final: 0.8668 (mp0)
REVERT: K   20 MET cc_start: 0.7574 (mmp) cc_final: 0.7251 (mmp)
REVERT: L   60 TYR cc_start: 0.7503 (t80) cc_final: 0.7089 (t80)
REVERT: L  134 TYR cc_start: 0.6623 (t80) cc_final: 0.6064 (t80)
REVERT: M    1 MET cc_start: 0.5532 (tmm) cc_final: 0.5240 (tmm)
  outliers start: 16
  outliers final: 12
  residues processed: 234
  average time/residue: 0.1280
  time to fit residues: 42.7293
Evaluate side-chains
  223 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 210
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0570
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   chunk 128 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
F  25 ASN
G  38 ASN
H  47 GLN
K  41 GLN
L  55 HIS
M  25 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.119651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.084196 restraints weight = 61636.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.087543 restraints weight = 48177.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.087057 restraints weight = 25569.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.087707 restraints weight = 19345.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.088300 restraints weight = 17267.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15482  Z= 0.150
  Angle     :  0.649  11.544  22186  Z= 0.369
  Chirality :  0.042   0.265   2516
  Planarity :  0.004   0.060   1794
  Dihedral  : 29.216 176.768   4413
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.32 %
    Favored  : 80.19 %
  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:  1.93 (0.27), residues: 1057
  helix:  2.44 (0.21), residues: 651
  sheet: -0.03 (0.66), residues: 49
  loop : -0.76 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.020   0.002   TYR L 134 
 PHE   0.014   0.001   PHE M  45 
 TRP   0.062   0.004   TRP L 141 
 HIS   0.004   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.15 (15472)
  covalent geometry    : angle       0.63971 /  0.37 (22171)
  hydrogen bonds       : bond        0.04954 /  3.28 (  848)
  hydrogen bonds       : angle       3.40113 /  2.42 ( 2154)
  metal coordination   : bond        0.01347 /  0.67 (    8)
  metal coordination   : angle       5.60054 /  2.42 (    9)
  link_TRANS           : bond        0.00079 /  0.04 (    2)
  link_TRANS           : angle       0.31795 /  0.14 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 223
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9179 (t) cc_final: 0.8048 (t)
REVERT: A   59 GLU cc_start: 0.8858 (pm20) cc_final: 0.8122 (pm20)
REVERT: A   60 LEU cc_start: 0.9202 (mt) cc_final: 0.8901 (mt)
REVERT: A  125 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7130 (pm20)
REVERT: C  110 ASN cc_start: 0.8674 (p0) cc_final: 0.8459 (p0)
REVERT: D  108 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8030 (mtpt)
REVERT: F   88 TYR cc_start: 0.8790 (m-80) cc_final: 0.8381 (m-80)
REVERT: H   35 GLU cc_start: 0.8946 (mp0) cc_final: 0.8596 (mp0)
REVERT: L  111 ASP cc_start: 0.8244 (m-30) cc_final: 0.7931 (m-30)
REVERT: L  144 LYS cc_start: 0.8914 (pttm) cc_final: 0.8652 (pttm)
REVERT: M    1 MET cc_start: 0.5346 (tmm) cc_final: 0.5099 (tmm)
  outliers start: 22
  outliers final: 18
  residues processed: 233
  average time/residue: 0.1403
  time to fit residues: 46.3135
Evaluate side-chains
  234 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 215
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   36 THR
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain M residue   17 VAL
Chi-restraints excluded: chain M residue   52 ASP
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 78 optimal weight:    9.9990
   chunk 10 optimal weight:    0.6980
   chunk 87 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 126 optimal weight:    0.0980
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  38 ASN
K  32 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 ASN
L  46 GLN
L  55 HIS
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  25 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.119597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.082056 restraints weight = 51823.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.082753 restraints weight = 32208.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.083206 restraints weight = 24681.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.083914 restraints weight = 18095.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.083970 restraints weight = 16960.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15482  Z= 0.148
  Angle     :  0.644  12.076  22186  Z= 0.366
  Chirality :  0.042   0.266   2516
  Planarity :  0.004   0.062   1794
  Dihedral  : 29.249 176.707   4413
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.29 %
    Favored  : 79.33 %
  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:  1.97 (0.27), residues: 1057
  helix:  2.47 (0.21), residues: 652
  sheet:  0.07 (0.68), residues: 49
  loop : -0.77 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L 139 
 TYR   0.024   0.002   TYR L 134 
 PHE   0.011   0.001   PHE M  45 
 TRP   0.068   0.004   TRP L 141 
 HIS   0.003   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.15 (15472)
  covalent geometry    : angle       0.63488 /  0.37 (22171)
  hydrogen bonds       : bond        0.04824 /  3.18 (  848)
  hydrogen bonds       : angle       3.34649 /  2.39 ( 2154)
  metal coordination   : bond        0.01336 /  0.67 (    8)
  metal coordination   : angle       5.46114 /  2.39 (    9)
  link_TRANS           : bond        0.00075 /  0.04 (    2)
  link_TRANS           : angle       0.31580 /  0.13 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 232
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9118 (t) cc_final: 0.7854 (t)
REVERT: A   59 GLU cc_start: 0.8845 (pm20) cc_final: 0.8143 (pm20)
REVERT: A   60 LEU cc_start: 0.9181 (mt) cc_final: 0.8922 (mt)
REVERT: A  123 ASP cc_start: 0.8912 (m-30) cc_final: 0.8662 (m-30)
REVERT: A  125 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7141 (pm20)
REVERT: B   63 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: B   67 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7992 (ttp-170)
REVERT: C  110 ASN cc_start: 0.8753 (p0) cc_final: 0.8502 (p0)
REVERT: D  108 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8045 (mtmt)
REVERT: F   88 TYR cc_start: 0.8928 (m-10) cc_final: 0.8500 (m-80)
REVERT: H   35 GLU cc_start: 0.8942 (mp0) cc_final: 0.8569 (mp0)
REVERT: K   41 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9022 (mm-40)
REVERT: L  134 TYR cc_start: 0.6872 (t80) cc_final: 0.6665 (t80)
REVERT: L  139 ARG cc_start: 0.8895 (mmt-90) cc_final: 0.8565 (mpt180)
  outliers start: 21
  outliers final: 16
  residues processed: 243
  average time/residue: 0.1365
  time to fit residues: 46.9001
Evaluate side-chains
  237 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 220
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain M residue   52 ASP
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 122 optimal weight:    0.0970
   chunk 32 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0980
   chunk 110 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
K  32 ASN
K  41 GLN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  55 HIS
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  25 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.120350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.082783 restraints weight = 51711.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.084797 restraints weight = 32055.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.084300 restraints weight = 29849.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.084730 restraints weight = 19352.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.084898 restraints weight = 17164.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15482  Z= 0.147
  Angle     :  0.655  12.424  22186  Z= 0.369
  Chirality :  0.042   0.267   2516
  Planarity :  0.004   0.056   1794
  Dihedral  : 29.270 176.636   4413
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.59 %
    Favored  : 78.03 %
  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 (0.27), residues: 1057
  helix:  2.48 (0.21), residues: 652
  sheet:  0.09 (0.70), residues: 49
  loop : -0.78 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.017   0.002   TYR E  99 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.064   0.004   TRP L 141 
 HIS   0.006   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.15 (15472)
  covalent geometry    : angle       0.64569 /  0.37 (22171)
  hydrogen bonds       : bond        0.04733 /  3.11 (  848)
  hydrogen bonds       : angle       3.31471 /  2.36 ( 2154)
  metal coordination   : bond        0.01307 /  0.65 (    8)
  metal coordination   : angle       5.50838 /  2.40 (    9)
  link_TRANS           : bond        0.00077 /  0.04 (    2)
  link_TRANS           : angle       0.29778 /  0.12 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 228
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9091 (t) cc_final: 0.7822 (t)
REVERT: A   59 GLU cc_start: 0.8827 (pm20) cc_final: 0.8109 (pm20)
REVERT: A   60 LEU cc_start: 0.9177 (mt) cc_final: 0.8935 (mt)
REVERT: A  123 ASP cc_start: 0.8899 (m-30) cc_final: 0.8637 (m-30)
REVERT: A  125 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7136 (pm20)
REVERT: B   63 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8182 (mt-10)
REVERT: B   67 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7973 (ttp-170)
REVERT: C  110 ASN cc_start: 0.8738 (p0) cc_final: 0.8506 (p0)
REVERT: D  108 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8038 (mtmt)
REVERT: F   88 TYR cc_start: 0.8927 (m-10) cc_final: 0.8481 (m-80)
REVERT: H   35 GLU cc_start: 0.8925 (mp0) cc_final: 0.8574 (mp0)
REVERT: L  111 ASP cc_start: 0.8198 (m-30) cc_final: 0.7887 (m-30)
REVERT: L  144 LYS cc_start: 0.8736 (pttm) cc_final: 0.8422 (pttm)
REVERT: M    1 MET cc_start: 0.5249 (tmm) cc_final: 0.5043 (tmm)
  outliers start: 21
  outliers final: 15
  residues processed: 238
  average time/residue: 0.1414
  time to fit residues: 47.8292
Evaluate side-chains
  236 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 220
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   45 TYR
Chi-restraints excluded: chain M residue   52 ASP
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 94 optimal weight:   10.0000
   chunk 81 optimal weight:   10.9990
   chunk 62 optimal weight:    0.0060
   chunk 23 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.6998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
K  32 ASN
K  41 GLN
L   7 ASN
L  55 HIS
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 135 ASN
M  25 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.120006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.083527 restraints weight = 54219.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.085141 restraints weight = 36338.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.084852 restraints weight = 33641.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.085410 restraints weight = 20634.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.085908 restraints weight = 18199.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15482  Z= 0.151
  Angle     :  0.665  12.984  22186  Z= 0.372
  Chirality :  0.042   0.269   2516
  Planarity :  0.005   0.070   1794
  Dihedral  : 29.303 176.457   4413
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.56 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.27), residues: 1057
  helix:  2.51 (0.21), residues: 652
  sheet:  0.15 (0.71), residues: 49
  loop : -0.78 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  31 
 TYR   0.022   0.002   TYR L 134 
 PHE   0.010   0.001   PHE L  62 
 TRP   0.079   0.005   TRP L 141 
 HIS   0.004   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.15 (15472)
  covalent geometry    : angle       0.65565 /  0.37 (22171)
  hydrogen bonds       : bond        0.04724 /  3.11 (  848)
  hydrogen bonds       : angle       3.30634 /  2.36 ( 2154)
  metal coordination   : bond        0.01338 /  0.67 (    8)
  metal coordination   : angle       5.54854 /  2.42 (    9)
  link_TRANS           : bond        0.00065 /  0.03 (    2)
  link_TRANS           : angle       0.30085 /  0.12 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 228
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9076 (t) cc_final: 0.7791 (t)
REVERT: A   59 GLU cc_start: 0.8800 (pm20) cc_final: 0.8088 (pm20)
REVERT: A   60 LEU cc_start: 0.9195 (mt) cc_final: 0.8944 (mt)
REVERT: A  123 ASP cc_start: 0.8881 (m-30) cc_final: 0.8620 (m-30)
REVERT: A  125 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7152 (pm20)
REVERT: B   25 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8306 (t160)
REVERT: B   63 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: B   67 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7960 (ttp-170)
REVERT: D  108 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8048 (mtmt)
REVERT: F   88 TYR cc_start: 0.8866 (m-10) cc_final: 0.8417 (m-80)
REVERT: H   35 GLU cc_start: 0.8909 (mp0) cc_final: 0.8576 (mp0)
REVERT: L   31 PHE cc_start: 0.8067 (m-10) cc_final: 0.7660 (m-80)
REVERT: L  144 LYS cc_start: 0.8833 (pttm) cc_final: 0.8431 (pttm)
  outliers start: 25
  outliers final: 18
  residues processed: 240
  average time/residue: 0.1296
  time to fit residues: 44.7468
Evaluate side-chains
  238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 218
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain M residue   52 ASP
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 120 optimal weight:    0.9980
   chunk 116 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 127 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 100 optimal weight:    0.1980
   chunk 94 optimal weight:    9.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
K  32 ASN
K  41 GLN
L  55 HIS
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  25 ASN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.120172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.084168 restraints weight = 58689.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.087709 restraints weight = 46980.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.087050 restraints weight = 25825.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.087742 restraints weight = 19367.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.088166 restraints weight = 17357.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15482  Z= 0.150
  Angle     :  0.685  13.029  22186  Z= 0.377
  Chirality :  0.042   0.268   2516
  Planarity :  0.004   0.060   1794
  Dihedral  : 29.326 176.313   4413
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.75 %
    Favored  : 75.65 %
  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:  1.96 (0.27), residues: 1057
  helix:  2.47 (0.21), residues: 652
  sheet:  0.27 (0.70), residues: 48
  loop : -0.83 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.023   0.002   TYR L 134 
 PHE   0.010   0.001   PHE M  45 
 TRP   0.076   0.004   TRP L 141 
 HIS   0.003   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 (15472)
  covalent geometry    : angle       0.67567 /  0.38 (22171)
  hydrogen bonds       : bond        0.04686 /  3.09 (  848)
  hydrogen bonds       : angle       3.31058 /  2.37 ( 2154)
  metal coordination   : bond        0.01355 /  0.68 (    8)
  metal coordination   : angle       5.55184 /  2.43 (    9)
  link_TRANS           : bond        0.00069 /  0.03 (    2)
  link_TRANS           : angle       0.31320 /  0.13 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 226
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9079 (t) cc_final: 0.7809 (t)
REVERT: A   59 GLU cc_start: 0.8784 (pm20) cc_final: 0.8070 (pm20)
REVERT: A   60 LEU cc_start: 0.9219 (mt) cc_final: 0.8952 (mt)
REVERT: A   76 GLN cc_start: 0.8578 (pp30) cc_final: 0.8338 (pp30)
REVERT: A  123 ASP cc_start: 0.8954 (m-30) cc_final: 0.8718 (m-30)
REVERT: A  125 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7118 (pm20)
REVERT: B   27 GLN cc_start: 0.8852 (mp-120) cc_final: 0.8588 (mp10)
REVERT: B   63 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8091 (mt-10)
REVERT: B   67 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7953 (ttp-170)
REVERT: C   13 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7834 (mptt)
REVERT: D  108 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8024 (mtmt)
REVERT: F   88 TYR cc_start: 0.8853 (m-10) cc_final: 0.8465 (m-10)
REVERT: H   35 GLU cc_start: 0.8916 (mp0) cc_final: 0.8589 (mp0)
REVERT: L   31 PHE cc_start: 0.7940 (m-10) cc_final: 0.7572 (m-80)
REVERT: L  111 ASP cc_start: 0.8089 (m-30) cc_final: 0.7811 (m-30)
REVERT: L  144 LYS cc_start: 0.8836 (pttm) cc_final: 0.8481 (pttm)
REVERT: M    1 MET cc_start: 0.5779 (tmm) cc_final: 0.5177 (tpt)
  outliers start: 23
  outliers final: 18
  residues processed: 236
  average time/residue: 0.1329
  time to fit residues: 44.8333
Evaluate side-chains
  241 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 222
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain M residue   52 ASP
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 87 optimal weight:   20.0000
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
K  32 ASN
K  41 GLN
L  55 HIS
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  25 ASN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.119842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.080131 restraints weight = 45779.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.080551 restraints weight = 26950.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.080761 restraints weight = 26441.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.081037 restraints weight = 20024.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.082257 restraints weight = 17575.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15482  Z= 0.153
  Angle     :  0.686  13.464  22186  Z= 0.379
  Chirality :  0.042   0.270   2516
  Planarity :  0.004   0.060   1794
  Dihedral  : 29.368 176.138   4413
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.19 %
    Favored  : 75.54 %
  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:  1.93 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 653
  sheet:  0.33 (0.71), residues: 48
  loop : -0.82 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.025   0.002   TYR L 127 
 PHE   0.009   0.001   PHE L  62 
 TRP   0.071   0.004   TRP L 141 
 HIS   0.003   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.15 (15472)
  covalent geometry    : angle       0.67651 /  0.38 (22171)
  hydrogen bonds       : bond        0.04710 /  3.11 (  848)
  hydrogen bonds       : angle       3.33866 /  2.39 ( 2154)
  metal coordination   : bond        0.01435 /  0.72 (    8)
  metal coordination   : angle       5.60348 /  2.47 (    9)
  link_TRANS           : bond        0.00055 /  0.03 (    2)
  link_TRANS           : angle       0.31673 /  0.12 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 224
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9051 (t) cc_final: 0.7688 (t)
REVERT: A   59 GLU cc_start: 0.8785 (pm20) cc_final: 0.8085 (pm20)
REVERT: A   60 LEU cc_start: 0.9178 (mt) cc_final: 0.8942 (mt)
REVERT: A   76 GLN cc_start: 0.8589 (pp30) cc_final: 0.8356 (pp30)
REVERT: A  123 ASP cc_start: 0.8846 (m-30) cc_final: 0.8580 (m-30)
REVERT: A  125 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7274 (pm20)
REVERT: B   63 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8151 (mt-10)
REVERT: B   67 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7939 (ttp-170)
REVERT: D  108 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8091 (mtmt)
REVERT: D  116 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8626 (ttpt)
REVERT: E   37 LYS cc_start: 0.8985 (tttm) cc_final: 0.8721 (tmtt)
REVERT: F   84 MET cc_start: 0.8790 (mmm) cc_final: 0.8500 (mmm)
REVERT: F   88 TYR cc_start: 0.9031 (m-10) cc_final: 0.8668 (m-10)
REVERT: G   36 LYS cc_start: 0.8680 (tppt) cc_final: 0.8439 (tppt)
REVERT: H   35 GLU cc_start: 0.8967 (mp0) cc_final: 0.8591 (mp0)
REVERT: K   41 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8973 (tp40)
REVERT: K   84 TYR cc_start: 0.7839 (m-80) cc_final: 0.6954 (m-80)
REVERT: L   31 PHE cc_start: 0.8091 (m-10) cc_final: 0.7629 (m-80)
REVERT: L   56 PHE cc_start: 0.8132 (m-80) cc_final: 0.7916 (m-80)
REVERT: L  144 LYS cc_start: 0.8970 (pttm) cc_final: 0.8681 (pttm)
REVERT: M    1 MET cc_start: 0.5944 (tmm) cc_final: 0.5387 (tpt)
  outliers start: 20
  outliers final: 17
  residues processed: 232
  average time/residue: 0.1217
  time to fit residues: 40.3990
Evaluate side-chains
  240 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 221
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain M residue   52 ASP
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 111 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 121 optimal weight:    0.8980
   chunk 86 optimal weight:   10.0000
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
K  32 ASN
K  41 GLN
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.120124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.084535 restraints weight = 61900.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.087803 restraints weight = 50157.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.087423 restraints weight = 25905.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.087935 restraints weight = 19956.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.088663 restraints weight = 17894.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  15482  Z= 0.153
  Angle     :  0.689  13.699  22186  Z= 0.379
  Chirality :  0.042   0.270   2516
  Planarity :  0.005   0.060   1794
  Dihedral  : 29.374 176.137   4413
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.29 %
    Favored  : 75.54 %
  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:  1.91 (0.27), residues: 1057
  helix:  2.41 (0.21), residues: 653
  sheet:  0.37 (0.73), residues: 48
  loop : -0.83 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.045   0.002   TYR L 127 
 PHE   0.021   0.001   PHE K  40 
 TRP   0.079   0.004   TRP L 141 
 HIS   0.003   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.15 (15472)
  covalent geometry    : angle       0.67963 /  0.38 (22171)
  hydrogen bonds       : bond        0.04692 /  3.10 (  848)
  hydrogen bonds       : angle       3.34369 /  2.39 ( 2154)
  metal coordination   : bond        0.01487 /  0.74 (    8)
  metal coordination   : angle       5.68212 /  2.49 (    9)
  link_TRANS           : bond        0.00073 /  0.03 (    2)
  link_TRANS           : angle       0.31218 /  0.12 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 223
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9044 (t) cc_final: 0.7694 (t)
REVERT: A   59 GLU cc_start: 0.8775 (pm20) cc_final: 0.8064 (pm20)
REVERT: A   60 LEU cc_start: 0.9217 (mt) cc_final: 0.8949 (mt)
REVERT: A   76 GLN cc_start: 0.8629 (pp30) cc_final: 0.8392 (pp30)
REVERT: A  123 ASP cc_start: 0.8919 (m-30) cc_final: 0.8666 (m-30)
REVERT: A  125 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7136 (pm20)
REVERT: B   63 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8087 (mt-10)
REVERT: B   67 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7945 (ttp-170)
REVERT: C   13 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7625 (mptt)
REVERT: D   59 MET cc_start: 0.8344 (tpp) cc_final: 0.7819 (tpp)
REVERT: D  108 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8000 (mtmt)
REVERT: D  116 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8639 (ttpt)
REVERT: E   37 LYS cc_start: 0.8987 (tttm) cc_final: 0.8722 (tmtt)
REVERT: F   84 MET cc_start: 0.8658 (mmm) cc_final: 0.8356 (mmm)
REVERT: F   88 TYR cc_start: 0.8907 (m-10) cc_final: 0.8485 (m-10)
REVERT: G   36 LYS cc_start: 0.8690 (tppt) cc_final: 0.8433 (tppt)
REVERT: H   35 GLU cc_start: 0.8905 (mp0) cc_final: 0.8579 (mp0)
REVERT: K   21 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6691 (mm-30)
REVERT: K   41 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8735 (tp40)
REVERT: K   84 TYR cc_start: 0.7815 (m-80) cc_final: 0.6857 (m-80)
REVERT: L   31 PHE cc_start: 0.7949 (m-10) cc_final: 0.7548 (m-80)
REVERT: L  144 LYS cc_start: 0.8874 (pttm) cc_final: 0.8606 (pttm)
REVERT: M    1 MET cc_start: 0.5791 (tmm) cc_final: 0.5211 (tpt)
  outliers start: 19
  outliers final: 17
  residues processed: 231
  average time/residue: 0.1283
  time to fit residues: 42.0766
Evaluate side-chains
  240 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 221
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   41 GLN
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain M residue   52 ASP
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 128 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 113 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 87 optimal weight:   20.0000
   chunk 123 optimal weight:    5.9990
   chunk 127 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
K  32 ASN
K  41 GLN
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.119458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.082570 restraints weight = 53938.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.083513 restraints weight = 36410.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.083256 restraints weight = 37083.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.084232 restraints weight = 21242.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.084649 restraints weight = 18148.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15482  Z= 0.163
  Angle     :  0.694  13.393  22186  Z= 0.382
  Chirality :  0.042   0.271   2516
  Planarity :  0.005   0.058   1794
  Dihedral  : 29.392 176.029   4413
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.40 %
    Favored  : 75.32 %
  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:  1.86 (0.27), residues: 1057
  helix:  2.35 (0.21), residues: 654
  sheet:  0.33 (0.73), residues: 48
  loop : -0.81 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.029   0.002   TYR L 127 
 PHE   0.009   0.001   PHE K  40 
 TRP   0.078   0.004   TRP L 141 
 HIS   0.003   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 (15472)
  covalent geometry    : angle       0.68471 /  0.38 (22171)
  hydrogen bonds       : bond        0.04780 /  3.17 (  848)
  hydrogen bonds       : angle       3.41754 /  2.45 ( 2154)
  metal coordination   : bond        0.01533 /  0.76 (    8)
  metal coordination   : angle       5.74042 /  2.56 (    9)
  link_TRANS           : bond        0.00093 /  0.04 (    2)
  link_TRANS           : angle       0.34977 /  0.14 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2342.12 seconds
wall clock time: 41 minutes 7.17 seconds (2467.17 seconds total)