Starting phenix.real_space_refine
on Fri Jul  3 13:01:48 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn5_40613/07_2026/8sn5_40613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn5_40613/07_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_40613/07_2026/8sn5_40613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn5_40613/07_2026/8sn5_40613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn5_40613/07_2026/8sn5_40613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn5_40613/07_2026/8sn5_40613.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sn5_40613/07_2026/8sn5_40613.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sn5_40613/07_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-dev-6108/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: 2.50, per 1000 atoms: 0.17
  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: 0.87
  Conformation dependent library (CDL) restraints added in 447.2 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: 1.66
  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: 2.55

  Time building geometry restraints manager: 1.26 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: 20959
        1.54 -     3.07: 1133
        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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     14.210
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.800
-------------------------------------------------------------------------------
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= 0.472
  Angle     :  0.713   7.753  22186  Z= 0.604
  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       0.70901 /  0.60 (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  : 0.251 
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: 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: 0.8516 (m-80)
REVERT: D  108 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8001 (mtmt)
REVERT: H   35 GLU cc_start: 0.8641 (mp0) cc_final: 0.8421 (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: 0.8139 (tm-30)
REVERT: L   60 TYR cc_start: 0.7143 (t80) cc_final: 0.6810 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1319
  time to fit residues: 51.5705
Evaluate side-chains
  226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   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
G  38 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  81 GLN
K  83 HIS
L  46 GLN
M   2 GLN
M  25 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.117733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.080265 restraints weight = 53948.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.081991 restraints weight = 34329.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.081443 restraints weight = 34195.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.082062 restraints weight = 20896.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.082444 restraints weight = 18210.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    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 = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (14 function evaluations)
r_final: 0.2990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087  15482  Z= 0.251
  Angle     :  0.716  10.301  22186  Z= 0.405
  Chirality :  0.045   0.256   2516
  Planarity :  0.005   0.058   1794
  Dihedral  : 29.124 175.638   4413
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.42 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.27), residues: 1057
  helix:  2.38 (0.21), residues: 652
  sheet:  0.52 (0.69), residues: 50
  loop : -0.77 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  86 
 TYR   0.026   0.003   TYR L 127 
 PHE   0.014   0.002   PHE K  40 
 TRP   0.058   0.005   TRP L 141 
 HIS   0.005   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00554 /  0.25 (15472)
  covalent geometry    : angle       0.70667 /  0.40 (22171)
  hydrogen bonds       : bond        0.05898 /  3.92 (  848)
  hydrogen bonds       : angle       3.81026 /  2.71 ( 2154)
  metal coordination   : bond        0.01750 /  0.87 (    8)
  metal coordination   : angle       5.77001 /  2.62 (    9)
  link_TRANS           : bond        0.00211 /  0.10 (    2)
  link_TRANS           : angle       0.70327 /  0.27 (    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
  254 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 239
  time to evaluate  : 0.428 
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: 0.9189 (t) cc_final: 0.8059 (t)
REVERT: A   59 GLU cc_start: 0.8841 (pm20) cc_final: 0.7986 (pm20)
REVERT: A   60 LEU cc_start: 0.9241 (mt) cc_final: 0.8973 (mt)
REVERT: A  125 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7288 (pm20)
REVERT: C  110 ASN cc_start: 0.8674 (p0) cc_final: 0.8470 (p0)
REVERT: D  108 LYS cc_start: 0.8345 (ttpt) cc_final: 0.8100 (mtmt)
REVERT: F   88 TYR cc_start: 0.8895 (m-80) cc_final: 0.8502 (m-80)
REVERT: H   35 GLU cc_start: 0.8960 (mp0) cc_final: 0.8651 (mp0)
REVERT: L   60 TYR cc_start: 0.7501 (t80) cc_final: 0.7199 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 246
  average time/residue: 0.1322
  time to fit residues: 45.6183
Evaluate side-chains
  222 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 210
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 39 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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**
L   7 ASN
L  34 GLN
M  25 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.118713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.080041 restraints weight = 47305.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.079676 restraints weight = 29303.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.079893 restraints weight = 30924.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.080457 restraints weight = 21610.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.081421 restraints weight = 18595.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (14 function evaluations)
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.167
  Angle     :  0.665  11.266  22186  Z= 0.380
  Chirality :  0.043   0.305   2516
  Planarity :  0.004   0.063   1794
  Dihedral  : 29.215 176.203   4413
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.02 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 651
  sheet:  0.06 (0.67), residues: 50
  loop : -0.79 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.032   0.002   TYR L 145 
 PHE   0.014   0.001   PHE M  45 
 TRP   0.046   0.004   TRP L 141 
 HIS   0.004   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.17 (15472)
  covalent geometry    : angle       0.65505 /  0.38 (22171)
  hydrogen bonds       : bond        0.05302 /  3.50 (  848)
  hydrogen bonds       : angle       3.52931 /  2.52 ( 2154)
  metal coordination   : bond        0.01493 /  0.74 (    8)
  metal coordination   : angle       5.71354 /  2.51 (    9)
  link_TRANS           : bond        0.00117 /  0.06 (    2)
  link_TRANS           : angle       0.34461 /  0.15 (    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
  249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 229
  time to evaluate  : 0.419 
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: 0.9176 (t) cc_final: 0.8032 (t)
REVERT: A   59 GLU cc_start: 0.8923 (pm20) cc_final: 0.8163 (pm20)
REVERT: A   60 LEU cc_start: 0.9176 (mt) cc_final: 0.8953 (mt)
REVERT: A  125 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7326 (pm20)
REVERT: C  110 ASN cc_start: 0.8676 (p0) cc_final: 0.8457 (p0)
REVERT: D  108 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8116 (mtpt)
REVERT: F   88 TYR cc_start: 0.8910 (m-80) cc_final: 0.8585 (m-80)
REVERT: H   35 GLU cc_start: 0.8951 (mp0) cc_final: 0.8578 (mp0)
REVERT: L   60 TYR cc_start: 0.7523 (t80) cc_final: 0.7138 (t80)
REVERT: L  134 TYR cc_start: 0.6558 (t80) cc_final: 0.5998 (t80)
REVERT: M    1 MET cc_start: 0.5554 (tmm) cc_final: 0.5251 (tmm)
  outliers start: 20
  outliers final: 15
  residues processed: 238
  average time/residue: 0.1306
  time to fit residues: 44.2334
Evaluate side-chains
  232 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 216
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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  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 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 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:    0.9980
   chunk 73 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0570
   chunk 24 optimal weight:    0.4980
   chunk 128 optimal weight:    0.0470
   chunk 35 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.4396

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.119935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.084296 restraints weight = 61475.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.087845 restraints weight = 47439.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.087221 restraints weight = 25249.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.087866 restraints weight = 19236.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.088431 restraints weight = 17210.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    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 = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1601

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= 0.147
  Angle     :  0.637  11.693  22186  Z= 0.365
  Chirality :  0.042   0.242   2516
  Planarity :  0.004   0.061   1794
  Dihedral  : 29.280 176.402   4413
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.75 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.27), residues: 1057
  helix:  2.49 (0.21), residues: 651
  sheet:  0.06 (0.66), residues: 49
  loop : -0.75 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  33 
 TYR   0.017   0.002   TYR L 134 
 PHE   0.013   0.001   PHE M  45 
 TRP   0.061   0.004   TRP L 141 
 HIS   0.004   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.15 (15472)
  covalent geometry    : angle       0.62697 /  0.36 (22171)
  hydrogen bonds       : bond        0.04907 /  3.25 (  848)
  hydrogen bonds       : angle       3.37392 /  2.41 ( 2154)
  metal coordination   : bond        0.01324 /  0.66 (    8)
  metal coordination   : angle       5.59887 /  2.41 (    9)
  link_TRANS           : bond        0.00075 /  0.04 (    2)
  link_TRANS           : angle       0.27932 /  0.13 (    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
  241 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 225
  time to evaluate  : 0.387 
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: 0.9187 (t) cc_final: 0.8091 (t)
REVERT: A   59 GLU cc_start: 0.8856 (pm20) cc_final: 0.8121 (pm20)
REVERT: A   60 LEU cc_start: 0.9158 (mt) cc_final: 0.8913 (mt)
REVERT: A  125 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7120 (pm20)
REVERT: D  108 LYS cc_start: 0.8333 (ttpt) cc_final: 0.8022 (mtpt)
REVERT: F   88 TYR cc_start: 0.8784 (m-80) cc_final: 0.8206 (m-80)
REVERT: H   35 GLU cc_start: 0.8906 (mp0) cc_final: 0.8566 (mp0)
REVERT: L  111 ASP cc_start: 0.8208 (m-30) cc_final: 0.7831 (m-30)
REVERT: M    1 MET cc_start: 0.5281 (tmm) cc_final: 0.5045 (tmm)
  outliers start: 16
  outliers final: 13
  residues processed: 232
  average time/residue: 0.1280
  time to fit residues: 41.8444
Evaluate side-chains
  228 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 214
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
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 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   17 VAL
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:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 78 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 87 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 126 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0170
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7220

-------------------------------------------------------------------------------
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
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 = 0.3671 r_free = 0.3671 target = 0.119422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.082306 restraints weight = 52194.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.083340 restraints weight = 34038.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.083263 restraints weight = 33192.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.083868 restraints weight = 20690.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.084629 restraints weight = 18145.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
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   0.050  15482  Z= 0.152
  Angle     :  0.634  12.501  22186  Z= 0.362
  Chirality :  0.042   0.246   2516
  Planarity :  0.004   0.056   1794
  Dihedral  : 29.333 176.160   4413
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.86 %
    Favored  : 79.65 %
  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:  2.01 (0.27), residues: 1057
  helix:  2.49 (0.21), residues: 652
  sheet:  0.11 (0.68), residues: 49
  loop : -0.73 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 139 
 TYR   0.031   0.002   TYR L 134 
 PHE   0.010   0.001   PHE L  62 
 TRP   0.071   0.004   TRP L 141 
 HIS   0.003   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 (15472)
  covalent geometry    : angle       0.62403 /  0.36 (22171)
  hydrogen bonds       : bond        0.04835 /  3.18 (  848)
  hydrogen bonds       : angle       3.33987 /  2.38 ( 2154)
  metal coordination   : bond        0.01346 /  0.67 (    8)
  metal coordination   : angle       5.67306 /  2.46 (    9)
  link_TRANS           : bond        0.00070 /  0.03 (    2)
  link_TRANS           : angle       0.31306 /  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
  254 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 232
  time to evaluate  : 0.380 
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: 0.9116 (t) cc_final: 0.7863 (t)
REVERT: A   59 GLU cc_start: 0.8841 (pm20) cc_final: 0.8139 (pm20)
REVERT: A   60 LEU cc_start: 0.9175 (mt) cc_final: 0.8934 (mt)
REVERT: A  123 ASP cc_start: 0.8887 (m-30) cc_final: 0.8631 (m-30)
REVERT: A  125 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7165 (pm20)
REVERT: B   63 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8099 (mt-10)
REVERT: B   67 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7989 (ttp-170)
REVERT: C  110 ASN cc_start: 0.8586 (p0) cc_final: 0.8379 (p0)
REVERT: D  108 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8056 (mtmt)
REVERT: F   88 TYR cc_start: 0.8949 (m-10) cc_final: 0.8409 (m-80)
REVERT: H   31 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7713 (mtm-85)
REVERT: H   35 GLU cc_start: 0.8937 (mp0) cc_final: 0.8586 (mp0)
  outliers start: 22
  outliers final: 14
  residues processed: 244
  average time/residue: 0.1308
  time to fit residues: 44.9604
Evaluate side-chains
  232 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 217
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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  115 THR
Chi-restraints excluded: chain K residue   76 LEU
Chi-restraints excluded: chain L residue   26 VAL
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:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 122 optimal weight:    0.0170
   chunk 32 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0030
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.5028

-------------------------------------------------------------------------------
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
G  38 ASN
K  32 ASN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.120242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.083099 restraints weight = 52066.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.084369 restraints weight = 33647.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.084034 restraints weight = 33851.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.084881 restraints weight = 20377.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.085294 restraints weight = 17636.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
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 = 0.17   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 = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.145
  Angle     :  0.646  12.385  22186  Z= 0.365
  Chirality :  0.041   0.245   2516
  Planarity :  0.005   0.063   1794
  Dihedral  : 29.358 176.077   4413
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.48 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.27), residues: 1057
  helix:  2.51 (0.21), residues: 652
  sheet:  0.14 (0.70), residues: 49
  loop : -0.74 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG L 136 
 TYR   0.024   0.002   TYR L 134 
 PHE   0.011   0.001   PHE M  45 
 TRP   0.071   0.004   TRP L 141 
 HIS   0.005   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.15 (15472)
  covalent geometry    : angle       0.63622 /  0.36 (22171)
  hydrogen bonds       : bond        0.04720 /  3.11 (  848)
  hydrogen bonds       : angle       3.30061 /  2.35 ( 2154)
  metal coordination   : bond        0.01283 /  0.64 (    8)
  metal coordination   : angle       5.62754 /  2.42 (    9)
  link_TRANS           : bond        0.00063 /  0.03 (    2)
  link_TRANS           : angle       0.28116 /  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  : 0.425 
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: 0.9089 (t) cc_final: 0.7820 (t)
REVERT: A   59 GLU cc_start: 0.8822 (pm20) cc_final: 0.8111 (pm20)
REVERT: A   60 LEU cc_start: 0.9158 (mt) cc_final: 0.8918 (mt)
REVERT: A  123 ASP cc_start: 0.8874 (m-30) cc_final: 0.8620 (m-30)
REVERT: A  125 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7158 (pm20)
REVERT: B   63 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8081 (mt-10)
REVERT: B   67 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7964 (ttp-170)
REVERT: C  110 ASN cc_start: 0.8612 (p0) cc_final: 0.8370 (p0)
REVERT: D   33 ARG cc_start: 0.7294 (mtp-110) cc_final: 0.6795 (mtm110)
REVERT: D  108 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8049 (mtmt)
REVERT: F   88 TYR cc_start: 0.8963 (m-10) cc_final: 0.8459 (m-80)
REVERT: H   35 GLU cc_start: 0.8930 (mp0) cc_final: 0.8577 (mp0)
REVERT: L  111 ASP cc_start: 0.8176 (m-30) cc_final: 0.7859 (m-30)
REVERT: L  144 LYS cc_start: 0.8652 (pttm) cc_final: 0.8301 (pttm)
REVERT: M    1 MET cc_start: 0.5261 (tmm) cc_final: 0.5061 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 237
  average time/residue: 0.1340
  time to fit residues: 44.7710
Evaluate side-chains
  240 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 222
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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   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 L residue   45 TYR
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:    0.9980
   chunk 94 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0050
   chunk 23 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    0.1980
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.6194

-------------------------------------------------------------------------------
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**
M  25 ASN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.120311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.085398 restraints weight = 54427.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.088196 restraints weight = 56200.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.088000 restraints weight = 31697.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.088512 restraints weight = 23545.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.089056 restraints weight = 21277.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3095
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.147
  Angle     :  0.649  13.357  22186  Z= 0.366
  Chirality :  0.041   0.247   2516
  Planarity :  0.004   0.056   1794
  Dihedral  : 29.392 175.821   4413
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.35 %
    Favored  : 77.06 %
  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:  2.03 (0.27), residues: 1057
  helix:  2.52 (0.21), residues: 658
  sheet:  0.08 (0.71), residues: 49
  loop : -0.80 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.017   0.002   TYR E  99 
 PHE   0.010   0.001   PHE L  62 
 TRP   0.061   0.004   TRP L 141 
 HIS   0.004   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.15 (15472)
  covalent geometry    : angle       0.63932 /  0.37 (22171)
  hydrogen bonds       : bond        0.04677 /  3.09 (  848)
  hydrogen bonds       : angle       3.29379 /  2.35 ( 2154)
  metal coordination   : bond        0.01340 /  0.67 (    8)
  metal coordination   : angle       5.60013 /  2.43 (    9)
  link_TRANS           : bond        0.00060 /  0.03 (    2)
  link_TRANS           : angle       0.29293 /  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
  248 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 225
  time to evaluate  : 0.425 
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: 0.9026 (t) cc_final: 0.7735 (t)
REVERT: A   59 GLU cc_start: 0.8752 (pm20) cc_final: 0.8078 (pm20)
REVERT: A   60 LEU cc_start: 0.9146 (mt) cc_final: 0.8931 (mt)
REVERT: A   76 GLN cc_start: 0.8539 (pp30) cc_final: 0.8289 (pp30)
REVERT: A  123 ASP cc_start: 0.8925 (m-30) cc_final: 0.8663 (m-30)
REVERT: A  125 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7177 (pm20)
REVERT: B   25 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8231 (t160)
REVERT: B   63 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8123 (mt-10)
REVERT: B   67 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7979 (ttp-170)
REVERT: C  110 ASN cc_start: 0.8646 (p0) cc_final: 0.8424 (p0)
REVERT: D   33 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.6815 (mtm110)
REVERT: D  108 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8010 (mtmt)
REVERT: F   88 TYR cc_start: 0.8936 (m-10) cc_final: 0.8595 (m-10)
REVERT: G   36 LYS cc_start: 0.8693 (tppt) cc_final: 0.8431 (tppt)
REVERT: H   35 GLU cc_start: 0.8838 (mp0) cc_final: 0.8563 (mp0)
REVERT: L   31 PHE cc_start: 0.7794 (m-10) cc_final: 0.7507 (m-80)
REVERT: L  144 LYS cc_start: 0.8628 (pttm) cc_final: 0.8276 (pttm)
  outliers start: 23
  outliers final: 17
  residues processed: 236
  average time/residue: 0.1362
  time to fit residues: 45.6263
Evaluate side-chains
  237 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 218
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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 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 L residue   74 TYR
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:    0.4980
   chunk 64 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0970
   chunk 120 optimal weight:    1.9990
   chunk 116 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 127 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 94 optimal weight:   10.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.120456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.084605 restraints weight = 58852.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.087977 restraints weight = 46923.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.087485 restraints weight = 25462.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.087956 restraints weight = 19443.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.088862 restraints weight = 17561.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    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: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15482  Z= 0.147
  Angle     :  0.658  12.765  22186  Z= 0.368
  Chirality :  0.041   0.247   2516
  Planarity :  0.004   0.057   1794
  Dihedral  : 29.418 175.766   4413
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.89 %
    Favored  : 76.52 %
  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:  2.02 (0.27), residues: 1057
  helix:  2.51 (0.21), residues: 658
  sheet:  0.29 (0.71), residues: 48
  loop : -0.85 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.052   0.002   TYR L 145 
 PHE   0.009   0.001   PHE M  45 
 TRP   0.082   0.004   TRP L 141 
 HIS   0.003   0.001   HIS K  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.15 (15472)
  covalent geometry    : angle       0.64821 /  0.37 (22171)
  hydrogen bonds       : bond        0.04654 /  3.08 (  848)
  hydrogen bonds       : angle       3.29105 /  2.35 ( 2154)
  metal coordination   : bond        0.01342 /  0.67 (    8)
  metal coordination   : angle       5.61311 /  2.43 (    9)
  link_TRANS           : bond        0.00058 /  0.03 (    2)
  link_TRANS           : angle       0.30314 /  0.12 (    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
  243 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 220
  time to evaluate  : 0.421 
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: 0.9065 (t) cc_final: 0.7749 (t)
REVERT: A   59 GLU cc_start: 0.8780 (pm20) cc_final: 0.8066 (pm20)
REVERT: A   60 LEU cc_start: 0.9217 (mt) cc_final: 0.8953 (mt)
REVERT: A   76 GLN cc_start: 0.8574 (pp30) cc_final: 0.8331 (pp30)
REVERT: A  123 ASP cc_start: 0.8901 (m-30) cc_final: 0.8663 (m-30)
REVERT: A  125 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7084 (pm20)
REVERT: B   27 GLN cc_start: 0.8856 (mp-120) cc_final: 0.8596 (mp10)
REVERT: B   63 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8085 (mt-10)
REVERT: B   67 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7955 (ttp-170)
REVERT: C   13 LYS cc_start: 0.8148 (mmmm) cc_final: 0.7810 (mptt)
REVERT: D   33 ARG cc_start: 0.7372 (mtp-110) cc_final: 0.6901 (mtm110)
REVERT: D  108 LYS cc_start: 0.8340 (ttpt) cc_final: 0.8011 (mtmt)
REVERT: F   88 TYR cc_start: 0.8884 (m-10) cc_final: 0.8487 (m-10)
REVERT: G   36 LYS cc_start: 0.8715 (tppt) cc_final: 0.8430 (tppt)
REVERT: H   35 GLU cc_start: 0.8950 (mp0) cc_final: 0.8626 (mp0)
REVERT: L   31 PHE cc_start: 0.7950 (m-10) cc_final: 0.7581 (m-80)
REVERT: L  111 ASP cc_start: 0.8131 (m-30) cc_final: 0.7861 (m-30)
REVERT: L  144 LYS cc_start: 0.8761 (pttm) cc_final: 0.8434 (pttm)
REVERT: M    1 MET cc_start: 0.5782 (tmm) cc_final: 0.5178 (tpt)
  outliers start: 23
  outliers final: 18
  residues processed: 231
  average time/residue: 0.1323
  time to fit residues: 43.4482
Evaluate side-chains
  237 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 218
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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 L residue   74 TYR
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:    7.9990
   chunk 72 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 87 optimal weight:   20.0000
   chunk 13 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 56 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.120895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.081594 restraints weight = 45659.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.081716 restraints weight = 27372.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.081980 restraints weight = 27215.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.082396 restraints weight = 20083.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.083122 restraints weight = 17647.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2059

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= 0.145
  Angle     :  0.662  13.971  22186  Z= 0.369
  Chirality :  0.041   0.248   2516
  Planarity :  0.004   0.056   1794
  Dihedral  : 29.455 175.673   4413
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.54 %
    Favored  : 76.30 %
  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:  2.49 (0.21), residues: 660
  sheet:  0.18 (0.70), residues: 48
  loop : -0.82 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.052   0.002   TYR L 145 
 PHE   0.008   0.001   PHE M  45 
 TRP   0.073   0.004   TRP L 141 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.14 (15472)
  covalent geometry    : angle       0.65242 /  0.37 (22171)
  hydrogen bonds       : bond        0.04587 /  3.05 (  848)
  hydrogen bonds       : angle       3.28791 /  2.35 ( 2154)
  metal coordination   : bond        0.01352 /  0.68 (    8)
  metal coordination   : angle       5.60749 /  2.43 (    9)
  link_TRANS           : bond        0.00035 /  0.02 (    2)
  link_TRANS           : angle       0.31462 /  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: 19
    poor density    : 225
  time to evaluate  : 0.410 
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: 0.9018 (t) cc_final: 0.7660 (t)
REVERT: A   59 GLU cc_start: 0.8775 (pm20) cc_final: 0.8065 (pm20)
REVERT: A   60 LEU cc_start: 0.9164 (mt) cc_final: 0.8939 (mt)
REVERT: A   76 GLN cc_start: 0.8559 (pp30) cc_final: 0.8330 (pp30)
REVERT: A  123 ASP cc_start: 0.8823 (m-30) cc_final: 0.8557 (m-30)
REVERT: A  125 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7249 (pm20)
REVERT: B   63 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8155 (mt-10)
REVERT: B   67 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7925 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7399 (mtp-110) cc_final: 0.6954 (mtm110)
REVERT: D  108 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8090 (mtmt)
REVERT: F   88 TYR cc_start: 0.9017 (m-10) cc_final: 0.8680 (m-10)
REVERT: G   36 LYS cc_start: 0.8698 (tppt) cc_final: 0.8436 (tppt)
REVERT: H   35 GLU cc_start: 0.8952 (mp0) cc_final: 0.8587 (mp0)
REVERT: L   31 PHE cc_start: 0.8015 (m-10) cc_final: 0.7567 (m-80)
REVERT: M    1 MET cc_start: 0.5909 (tmm) cc_final: 0.5352 (tpt)
  outliers start: 19
  outliers final: 18
  residues processed: 234
  average time/residue: 0.1356
  time to fit residues: 44.7285
Evaluate side-chains
  239 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 220
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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 L residue   74 TYR
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:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 111 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 42 optimal weight:    0.2980
   chunk 121 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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  25 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.120295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.085020 restraints weight = 61870.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.088100 restraints weight = 47843.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.087543 restraints weight = 27598.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.088246 restraints weight = 19777.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.088741 restraints weight = 17714.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    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 = 0.3085 r_free = 0.3085    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: 0.3085
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  15482  Z= 0.155
  Angle     :  0.678  13.807  22186  Z= 0.375
  Chirality :  0.041   0.249   2516
  Planarity :  0.005   0.057   1794
  Dihedral  : 29.479 175.473   4413
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  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:  1.98 (0.27), residues: 1057
  helix:  2.47 (0.21), residues: 660
  sheet:  0.22 (0.71), residues: 48
  loop : -0.85 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  31 
 TYR   0.021   0.002   TYR D  83 
 PHE   0.009   0.001   PHE M  45 
 TRP   0.090   0.005   TRP L 141 
 HIS   0.003   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.15 (15472)
  covalent geometry    : angle       0.66866 /  0.37 (22171)
  hydrogen bonds       : bond        0.04704 /  3.11 (  848)
  hydrogen bonds       : angle       3.34825 /  2.39 ( 2154)
  metal coordination   : bond        0.01438 /  0.72 (    8)
  metal coordination   : angle       5.73683 /  2.51 (    9)
  link_TRANS           : bond        0.00050 /  0.02 (    2)
  link_TRANS           : angle       0.30140 /  0.11 (    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
  245 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 225
  time to evaluate  : 0.400 
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: 0.9068 (t) cc_final: 0.7725 (t)
REVERT: A   59 GLU cc_start: 0.8739 (pm20) cc_final: 0.7996 (pm20)
REVERT: A   60 LEU cc_start: 0.9219 (mt) cc_final: 0.8934 (mt)
REVERT: A   76 GLN cc_start: 0.8630 (pp30) cc_final: 0.8400 (pp30)
REVERT: A  123 ASP cc_start: 0.8932 (m-30) cc_final: 0.8693 (m-30)
REVERT: A  125 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7107 (pm20)
REVERT: B   63 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8072 (mt-10)
REVERT: B   67 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7942 (ttp-170)
REVERT: C   13 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7765 (mptt)
REVERT: D   59 MET cc_start: 0.8345 (tpp) cc_final: 0.7798 (tpp)
REVERT: D  108 LYS cc_start: 0.8340 (ttpt) cc_final: 0.8010 (mtmt)
REVERT: F   84 MET cc_start: 0.8818 (mmm) cc_final: 0.8531 (mmm)
REVERT: F   88 TYR cc_start: 0.8978 (m-10) cc_final: 0.8576 (m-10)
REVERT: G   36 LYS cc_start: 0.8704 (tppt) cc_final: 0.8414 (tppt)
REVERT: H   35 GLU cc_start: 0.8923 (mp0) cc_final: 0.8584 (mp0)
REVERT: H   51 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8179 (t0)
REVERT: K   41 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8922 (tp40)
REVERT: K   84 TYR cc_start: 0.7799 (m-80) cc_final: 0.6919 (m-80)
REVERT: L   31 PHE cc_start: 0.7994 (m-10) cc_final: 0.7562 (m-80)
REVERT: L  111 ASP cc_start: 0.7951 (m-30) cc_final: 0.7749 (m-30)
REVERT: M    1 MET cc_start: 0.5894 (tmm) cc_final: 0.5326 (tpt)
  outliers start: 20
  outliers final: 16
  residues processed: 233
  average time/residue: 0.1367
  time to fit residues: 45.1118
Evaluate side-chains
  238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 219
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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  115 LEU
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   74 TYR
Chi-restraints excluded: chain M residue   68 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
                        ^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
                  ^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
           ^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites
    pair_proxies = self.pair_proxies(
                   ^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8904 > 50:
  distance: 59 - 84:   4.484
  distance: 64 - 71:   3.807
  distance: 65 - 95:   3.916
  distance: 71 - 72:   3.859
  distance: 72 - 73:   3.132
  distance: 74 - 104:   3.545
  distance: 79 - 80:   5.204
  distance: 80 - 81:   3.814
  distance: 80 - 84:   7.997
  distance: 81 - 110:   4.298
  distance: 84 - 85:   6.719
  distance: 85 - 86:   5.267
  distance: 85 - 88:   4.777
  distance: 87 - 117:   3.494
  distance: 95 - 96:  12.313
  distance: 96 - 97:  13.871
  distance: 96 - 99:  26.649
  distance: 97 - 98:   3.517
  distance: 97 - 104:   6.581
  distance: 98 - 124:   3.160
  distance: 99 - 100:  56.890
  distance: 100 - 101:  26.349
  distance: 101 - 102:  45.124
  distance: 101 - 103:  19.786
  distance: 104 - 105:   4.067
  distance: 106 - 110:   3.437
  distance: 125 - 126:   4.063
  distance: 126 - 127:   3.329
  distance: 126 - 133:   3.572