Starting phenix.real_space_refine
on Thu Aug  6 10:53:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7i_38099/08_2026/8x7i_38099.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7i_38099/08_2026/8x7i_38099.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2026/8x7i_38099.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2026/8x7i_38099.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2026/8x7i_38099.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2026/8x7i_38099.map"
  }
  resolution = 3.27
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1119 atoms to isotropic.
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      28      5.16       5
     C    8076      2.51       5
     N    2655      2.21       5
     O    3245      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14300
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 845
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "K"
      Number of atoms: 1125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1125
          Classifications: {'peptide': 147}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "L"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 641
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 73}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "M"
      Number of atoms: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 413
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "L"
      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  13447  SG  CYS L  31      56.643  71.877  28.876  1.00218.04           S
  ATOM  13589  SG  CYS L  51      58.205  75.289  28.905  1.00210.14           S
  ATOM  13613  SG  CYS L  54      54.564  75.086  28.068  1.00213.50           S
  ATOM  13338  SG  CYS L  16      67.989  71.834  23.293  1.00283.03           S
  ATOM  13356  SG  CYS L  19      71.632  71.909  22.328  1.00282.47           S
  ATOM  13486  SG  CYS L  36      70.625  69.933  25.344  1.00253.66           S
  ATOM  13504  SG  CYS L  39      70.429  73.629  25.607  1.00248.31           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLY M  75 " occ=0.45
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.45
  Time building chain proxies: 3.23, per 1000 atoms: 0.23
  Number of scatterers: 14300
  At special positions: 0
  Unit cell: (118.14, 128.88, 112.77, 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      28     16.00
     P     294     15.00
     O    3245      8.00
     N    2655      7.00
     C    8076      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 463.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L 201 "
        pdb="ZN    ZN L 201 " - pdb=" ND1 HIS L  33 "
        pdb="ZN    ZN L 201 " - pdb=" SG  CYS L  51 "
        pdb="ZN    ZN L 201 " - pdb=" SG  CYS L  31 "
        pdb="ZN    ZN L 201 " - pdb=" SG  CYS L  54 "
      pdb="  ZN L 202 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  36 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  16 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  39 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  19 "
      Number of angles added : 9


  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2002

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 13 sheets defined
      62.3% alpha, 4.2% beta
      143 base pairs and 243 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.594A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.816A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.399A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.627A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 3.667A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.548A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.523A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.514A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.587A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.512A  pdb=" N   ALA D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    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: 3.548A  pdb=" N   THR H  96 " --> pdb=" O   ARG H  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 124
    Processing helix  chain 'K' and resid 2 through 16
    Processing helix  chain 'K' and resid 86 through 91
    Processing helix  chain 'K' and resid 98 through 112
    Processing helix  chain 'K' and resid 120 through 130
    Processing helix  chain 'K' and resid 130 through 145
    Processing helix  chain 'L' and resid 10 through 15
    Processing helix  chain 'L' and resid 36 through 47
      removed outlier: 4.833A  pdb=" N   GLU L  45 " --> pdb=" O   GLN L  41 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA L  47 " --> pdb=" O   THR L  43 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 58 through 69
      removed outlier: 3.757A  pdb=" N   ARG L  67 " --> pdb=" O   ARG L  63 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ARG L  68 " --> pdb=" O   TYR L  64 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 73 through 84
    Processing helix  chain 'M' and resid 22 through 35
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.869A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.469A  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 100 through 102
      removed outlier: 6.817A  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: 7.062A  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: 7.292A  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 32 through 38
    Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28
      removed outlier: 3.552A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  27 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 6

    484 hydrogen bonds defined for protein.
    1431 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      343 hydrogen bonds
      598 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      243 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3279
        1.33 -     1.45: 4408
        1.45 -     1.57: 6848
        1.57 -     1.69: 586
        1.69 -     1.81: 44
  Bond restraints: 15165
  Sorted by residual:
  bond pdb=" C3'  DA J -67 "
       pdb=" C2'  DA J -67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.17e+01
  bond pdb=" C3'  DG I   4 "
       pdb=" O3'  DG I   4 "
    ideal  model  delta    sigma   weight residual
    1.435  1.395  0.040 1.30e-02 5.92e+03 9.57e+00
  bond pdb=" C3'  DC I  61 "
       pdb=" C2'  DC I  61 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.97e+00
  bond pdb=" C3'  DG I  10 "
       pdb=" C2'  DG I  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.86e+00
  bond pdb=" C3'  DG I   0 "
       pdb=" C2'  DG I   0 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.44e+00
  ... (remaining 15160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 20312
        1.44 -     2.88: 1374
        2.88 -     4.32: 79
        4.32 -     5.76: 15
        5.76 -     7.20: 1
  Bond angle restraints: 21781
  Sorted by residual:
  angle pdb=" O4'  DC I -26 "
        pdb=" C4'  DC I -26 "
        pdb=" C3'  DC I -26 "
      ideal   model   delta    sigma   weight residual
     106.00  103.18    2.82 6.00e-01 2.78e+00 2.21e+01
  angle pdb=" N3   DT J -42 "
        pdb=" C4   DT J -42 "
        pdb=" O4   DT J -42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.61   -2.71 6.00e-01 2.78e+00 2.04e+01
  angle pdb=" N3   DT I -24 "
        pdb=" C4   DT I -24 "
        pdb=" O4   DT I -24 "
      ideal   model   delta    sigma   weight residual
     119.90  122.57   -2.67 6.00e-01 2.78e+00 1.99e+01
  angle pdb=" O4'  DA J  32 "
        pdb=" C4'  DA J  32 "
        pdb=" C3'  DA J  32 "
      ideal   model   delta    sigma   weight residual
     106.00  103.33    2.67 6.00e-01 2.78e+00 1.98e+01
  angle pdb=" N3   DT J  71 "
        pdb=" C4   DT J  71 "
        pdb=" O4   DT J  71 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.89e+01
  ... (remaining 21776 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.16: 7056
       35.16 -    70.32: 1302
       70.32 -   105.48: 11
      105.48 -   140.64: 1
      140.64 -   175.80: 2
  Dihedral angle restraints: 8372
    sinusoidal: 5285
      harmonic: 3087
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.20  175.80     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.69  161.31     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   84.74  135.26     1      3.50e+01 8.16e-04 1.34e+01
  ... (remaining 8369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1633
       0.040 -    0.080: 589
       0.080 -    0.120: 207
       0.120 -    0.160: 57
       0.160 -    0.200: 3
  Chirality restraints: 2489
  Sorted by residual:
  chirality pdb=" C3'  DT I -59 "
            pdb=" C4'  DT I -59 "
            pdb=" O3'  DT I -59 "
            pdb=" C2'  DT I -59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.53   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" C3'  DT I  33 "
            pdb=" C4'  DT I  33 "
            pdb=" O3'  DT I  33 "
            pdb=" C2'  DT I  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.56   -0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" C3'  DT J -39 "
            pdb=" C4'  DT J -39 "
            pdb=" O3'  DT J -39 "
            pdb=" C2'  DT J -39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.46e-01
  ... (remaining 2486 not shown)

  Planarity restraints: 1746
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU L   3 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO L   4 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO L   4 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L   4 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "    0.024 2.00e-02 2.50e+03   9.90e-03 2.69e+00
        pdb=" N9   DA I  47 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "   -0.007 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -35 "   -0.024 2.00e-02 2.50e+03   9.41e-03 2.66e+00
        pdb=" N9   DG I -35 "    0.019 2.00e-02 2.50e+03
        pdb=" C8   DG I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I -35 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6   DG I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG I -35 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1743 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 425
        2.65 -     3.22: 12761
        3.22 -     3.78: 27171
        3.78 -     4.34: 34185
        4.34 -     4.90: 49782
  Nonbonded interactions: 124324
  Sorted by model distance:
  nonbonded pdb=" N2   DG I  51 "
            pdb=" O2   DC J -51 "
     model   vdw
     2.093 2.496
  nonbonded pdb=" N2   DG I  46 "
            pdb=" O2   DC J -46 "
     model   vdw
     2.094 2.496
  nonbonded pdb=" O2   DC I  52 "
            pdb=" N2   DG J -52 "
     model   vdw
     2.109 2.496
  nonbonded pdb=" O2   DC I  40 "
            pdb=" N2   DG J -40 "
     model   vdw
     2.115 2.496
  nonbonded pdb=" O2   DC I -52 "
            pdb=" N2   DG J  52 "
     model   vdw
     2.122 2.496
  ... (remaining 124319 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' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and (resid 19 through 22 or (resid 23 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 24 through 101))
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and (resid 10 through 14 or resid 16 through 118))
  selection = (chain 'G' and (resid 10 through 14 or resid 16 through 118))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     16.690
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
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      :  0.007   0.046  15173  Z= 0.563
  Angle     :  0.739   7.198  21790  Z= 0.629
  Chirality :  0.048   0.200   2489
  Planarity :  0.004   0.053   1746
  Dihedral  : 25.488 175.796   6370
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.87 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  4.61 %
    Favored  : 93.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.53 (0.27), residues: 1033
  helix:  1.99 (0.21), residues: 656
  sheet: -0.84 (1.01), residues: 24
  loop : -0.72 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  88 
 TYR   0.008   0.001   TYR B  51 
 PHE   0.011   0.001   PHE E  67 
 TRP   0.010   0.002   TRP K  93 
 HIS   0.003   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00667 /  0.56 (15165)
  covalent geometry    : angle       0.73649 /  0.63 (21781)
  hydrogen bonds       : bond        0.13883 /  9.23 (  827)
  hydrogen bonds       : angle       4.47578 /  3.22 ( 2029)
  metal coordination   : bond        0.00525 /  0.21 (    8)
  metal coordination   : angle       2.98548 /  1.60 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 273
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8664 (tm-30)
REVERT: C   38 ASN cc_start: 0.8754 (m-40) cc_final: 0.7562 (m-40)
REVERT: C   68 ASN cc_start: 0.8990 (m-40) cc_final: 0.8672 (m-40)
REVERT: E   73 GLU cc_start: 0.8063 (tt0) cc_final: 0.7672 (tt0)
REVERT: E   94 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8308 (mm-30)
REVERT: E  115 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8944 (mppt)
REVERT: F   88 TYR cc_start: 0.8862 (m-10) cc_final: 0.6970 (m-10)
REVERT: F   91 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8971 (ttpt)
REVERT: G   61 GLU cc_start: 0.8624 (tp30) cc_final: 0.8342 (mm-30)
REVERT: D   93 GLU cc_start: 0.8250 (mp0) cc_final: 0.7960 (mp0)
REVERT: D  116 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8617 (mtpt)
REVERT: H   68 ASP cc_start: 0.8790 (t70) cc_final: 0.8487 (t0)
REVERT: H   72 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8848 (mtt180)
REVERT: K   38 MET cc_start: 0.8957 (mtt) cc_final: 0.8534 (tpt)
REVERT: K   62 PHE cc_start: 0.9102 (m-80) cc_final: 0.8870 (m-80)
REVERT: K   87 ASP cc_start: 0.8780 (p0) cc_final: 0.8482 (p0)
REVERT: K   92 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8579 (tp-100)
REVERT: K  120 VAL cc_start: 0.7361 (t) cc_final: 0.7125 (t)
REVERT: L   20 MET cc_start: 0.7447 (mmt) cc_final: 0.7150 (mmt)
REVERT: L   45 GLU cc_start: 0.8965 (pm20) cc_final: 0.8601 (pm20)
REVERT: L   60 SER cc_start: 0.8715 (m) cc_final: 0.8424 (m)
REVERT: L   73 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7141 (t0)
  outliers start: 16
  outliers final: 5
  residues processed: 285
  average time/residue: 0.1612
  time to fit residues: 62.1291
Evaluate side-chains
  207 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 199
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain L residue   14 CYS
Chi-restraints excluded: chain L residue   73 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:   20.0000
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:   30.0000
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:   30.0000
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
E  68 GLN
E  76 GLN
F  27 GLN
G  38 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
D  95 GLN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS
L  41 GLN
L  73 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.049412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033147 restraints weight = 81277.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 2.99
r_work: 0.2554 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2549 r_free = 0.2549    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2547 r_free = 0.2547    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.2547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15173  Z= 0.179
  Angle     :  0.682   9.875  21790  Z= 0.395
  Chirality :  0.045   0.323   2489
  Planarity :  0.005   0.056   1746
  Dihedral  : 29.604 174.964   4396
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.19 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.61 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.62 (0.27), residues: 1033
  helix:  2.06 (0.21), residues: 662
  sheet: -0.56 (1.12), residues: 18
  loop : -0.76 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 136 
 TYR   0.023   0.002   TYR H  83 
 PHE   0.014   0.002   PHE A  67 
 TRP   0.027   0.003   TRP K 141 
 HIS   0.004   0.001   HIS L  83 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.18 (15165)
  covalent geometry    : angle       0.68017 /  0.40 (21781)
  hydrogen bonds       : bond        0.09999 /  6.78 (  827)
  hydrogen bonds       : angle       3.72150 /  2.70 ( 2029)
  metal coordination   : bond        0.00672 /  0.28 (    8)
  metal coordination   : angle       2.40902 /  1.28 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9059 (pm20) cc_final: 0.8788 (pm20)
REVERT: A   73 GLU cc_start: 0.9453 (tm-30) cc_final: 0.9091 (tt0)
REVERT: A   94 GLU cc_start: 0.8948 (tp30) cc_final: 0.8716 (tp30)
REVERT: B   88 TYR cc_start: 0.9196 (m-10) cc_final: 0.8773 (m-80)
REVERT: C   24 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8820 (mp10)
REVERT: C   56 GLU cc_start: 0.9280 (tt0) cc_final: 0.8786 (tt0)
REVERT: C   68 ASN cc_start: 0.9102 (m-40) cc_final: 0.8699 (m-40)
REVERT: E   94 GLU cc_start: 0.9227 (mm-30) cc_final: 0.9009 (mm-30)
REVERT: E  115 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9248 (mppt)
REVERT: F   91 LYS cc_start: 0.9428 (ttmt) cc_final: 0.9084 (ttpt)
REVERT: G   61 GLU cc_start: 0.9090 (tp30) cc_final: 0.8862 (tp30)
REVERT: D   31 ARG cc_start: 0.7417 (mmp-170) cc_final: 0.6477 (mmm160)
REVERT: D   83 TYR cc_start: 0.8377 (m-10) cc_final: 0.8172 (m-10)
REVERT: D   93 GLU cc_start: 0.8871 (mp0) cc_final: 0.8522 (mp0)
REVERT: D  116 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.9127 (mtpt)
REVERT: H   33 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7669 (ttt90)
REVERT: H   68 ASP cc_start: 0.9251 (t70) cc_final: 0.9023 (t0)
REVERT: H   85 LYS cc_start: 0.9456 (mmtt) cc_final: 0.9105 (mmmt)
REVERT: H   88 THR cc_start: 0.9258 (m) cc_final: 0.9056 (m)
REVERT: K    1 MET cc_start: 0.7492 (tmm) cc_final: 0.7183 (tmm)
REVERT: K   16 ASP cc_start: 0.9271 (m-30) cc_final: 0.9026 (p0)
REVERT: K   38 MET cc_start: 0.9061 (mtt) cc_final: 0.8689 (tpt)
REVERT: K   69 PHE cc_start: 0.8693 (m-80) cc_final: 0.8417 (t80)
REVERT: K   87 ASP cc_start: 0.8983 (p0) cc_final: 0.8735 (p0)
REVERT: K   92 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8658 (tp-100)
REVERT: K  120 VAL cc_start: 0.7499 (t) cc_final: 0.7180 (t)
REVERT: L   20 MET cc_start: 0.7489 (mmt) cc_final: 0.7236 (mmt)
  outliers start: 24
  outliers final: 14
  residues processed: 245
  average time/residue: 0.1455
  time to fit residues: 49.2184
Evaluate side-chains
  234 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 218
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 75 optimal weight:   20.0000
   chunk 102 optimal weight:    0.0170
   chunk 98 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 72 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 64 optimal weight:   20.0000
   chunk 59 optimal weight:   20.0000
   overall best weight:    3.8026

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
G  84 GLN
D  95 GLN
** K  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.048634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.032178 restraints weight = 82666.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.2698 rms_B_bonded: 3.01
r_work: 0.2518 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2514
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2514 r_free = 0.2514    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2514 r_free = 0.2514    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2514
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  15173  Z= 0.240
  Angle     :  0.694  11.183  21790  Z= 0.395
  Chirality :  0.045   0.289   2489
  Planarity :  0.005   0.054   1746
  Dihedral  : 29.802 174.134   4393
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.07 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.03 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.58 (0.27), residues: 1033
  helix:  2.05 (0.21), residues: 662
  sheet: -1.29 (0.87), residues: 24
  loop : -0.75 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K 125 
 TYR   0.016   0.002   TYR H 121 
 PHE   0.013   0.002   PHE E  67 
 TRP   0.014   0.002   TRP K 141 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.24 (15165)
  covalent geometry    : angle       0.69052 /  0.40 (21781)
  hydrogen bonds       : bond        0.09088 /  6.18 (  827)
  hydrogen bonds       : angle       3.67898 /  2.69 ( 2029)
  metal coordination   : bond        0.01215 /  0.56 (    8)
  metal coordination   : angle       3.26682 /  1.77 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.423 
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   59 GLU cc_start: 0.9133 (pm20) cc_final: 0.8807 (pm20)
REVERT: A   73 GLU cc_start: 0.9481 (tm-30) cc_final: 0.9244 (tm-30)
REVERT: A   94 GLU cc_start: 0.8910 (tp30) cc_final: 0.8630 (tt0)
REVERT: A  125 GLN cc_start: 0.9294 (mt0) cc_final: 0.8227 (mt0)
REVERT: C   24 GLN cc_start: 0.9417 (mm-40) cc_final: 0.8837 (mp10)
REVERT: C   56 GLU cc_start: 0.9273 (tt0) cc_final: 0.9034 (tt0)
REVERT: E   94 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8992 (mm-30)
REVERT: E  115 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9245 (mppt)
REVERT: F   91 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9098 (ttpt)
REVERT: G   61 GLU cc_start: 0.9140 (tp30) cc_final: 0.8814 (tp30)
REVERT: D   31 ARG cc_start: 0.7298 (mmp-170) cc_final: 0.6229 (mmm160)
REVERT: D   93 GLU cc_start: 0.8911 (mp0) cc_final: 0.8608 (mp0)
REVERT: H   33 ARG cc_start: 0.8402 (mtp85) cc_final: 0.7731 (ttt90)
REVERT: H  105 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7872 (tm-30)
REVERT: H  106 LEU cc_start: 0.9410 (mt) cc_final: 0.9186 (mt)
REVERT: H  113 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8971 (mm-30)
REVERT: K    1 MET cc_start: 0.7486 (tmm) cc_final: 0.7125 (tmm)
REVERT: K   38 MET cc_start: 0.9077 (mtt) cc_final: 0.8676 (tpt)
REVERT: K   87 ASP cc_start: 0.9004 (p0) cc_final: 0.8776 (p0)
REVERT: K   92 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8767 (tp-100)
REVERT: K  120 VAL cc_start: 0.7505 (t) cc_final: 0.6896 (t)
REVERT: K  125 ARG cc_start: 0.8874 (mtm110) cc_final: 0.8542 (ptp-170)
REVERT: K  147 MET cc_start: 0.8782 (mtt) cc_final: 0.8347 (mpp)
REVERT: L   20 MET cc_start: 0.7513 (mmt) cc_final: 0.7171 (mmt)
REVERT: L   45 GLU cc_start: 0.9361 (pm20) cc_final: 0.8786 (pm20)
  outliers start: 22
  outliers final: 16
  residues processed: 219
  average time/residue: 0.1408
  time to fit residues: 43.2349
Evaluate side-chains
  217 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 200
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 117 optimal weight:   30.0000
   chunk 61 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9980
   chunk 69 optimal weight:   30.0000
   chunk 112 optimal weight:    9.9990
   chunk 99 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 122 optimal weight:    7.9990
   chunk 81 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   overall best weight:    4.9988

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.048130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.031563 restraints weight = 82231.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.2679 rms_B_bonded: 2.99
r_work: 0.2500 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2495 r_free = 0.2495    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2495 r_free = 0.2495    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2495
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  15173  Z= 0.289
  Angle     :  0.723  10.247  21790  Z= 0.406
  Chirality :  0.046   0.289   2489
  Planarity :  0.005   0.056   1746
  Dihedral  : 30.009 174.376   4385
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 15.69 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.56 (0.27), residues: 1033
  helix:  2.06 (0.20), residues: 656
  sheet: -1.20 (0.92), residues: 24
  loop : -0.79 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K   5 
 TYR   0.025   0.002   TYR D  83 
 PHE   0.013   0.002   PHE E  67 
 TRP   0.008   0.002   TRP K 141 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00589 /  0.29 (15165)
  covalent geometry    : angle       0.72037 /  0.41 (21781)
  hydrogen bonds       : bond        0.09057 /  6.18 (  827)
  hydrogen bonds       : angle       3.74254 /  2.74 ( 2029)
  metal coordination   : bond        0.00857 /  0.39 (    8)
  metal coordination   : angle       3.26415 /  1.79 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 0.426 
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   59 GLU cc_start: 0.9138 (pm20) cc_final: 0.8786 (pm20)
REVERT: A   73 GLU cc_start: 0.9492 (tm-30) cc_final: 0.9270 (tm-30)
REVERT: A   94 GLU cc_start: 0.8927 (tp30) cc_final: 0.8632 (tt0)
REVERT: B   23 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8260 (ptp90)
REVERT: C   24 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9147 (mm110)
REVERT: E   94 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8993 (mm-30)
REVERT: E  115 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9252 (mppt)
REVERT: F   91 LYS cc_start: 0.9450 (ttmt) cc_final: 0.9151 (ttpt)
REVERT: G   61 GLU cc_start: 0.9133 (tp30) cc_final: 0.8887 (tp30)
REVERT: G   64 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8920 (pp20)
REVERT: D   93 GLU cc_start: 0.8936 (mp0) cc_final: 0.8669 (mp0)
REVERT: H   33 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7740 (ttt90)
REVERT: H   83 TYR cc_start: 0.8596 (m-10) cc_final: 0.8242 (m-10)
REVERT: H  101 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8952 (mm)
REVERT: H  105 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: H  106 LEU cc_start: 0.9460 (mt) cc_final: 0.9189 (mt)
REVERT: H  113 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8991 (mm-30)
REVERT: K    1 MET cc_start: 0.7486 (tmm) cc_final: 0.7137 (tmm)
REVERT: K   38 MET cc_start: 0.9143 (mtt) cc_final: 0.8702 (tpt)
REVERT: K   87 ASP cc_start: 0.9010 (p0) cc_final: 0.8794 (p0)
REVERT: K   92 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8696 (tp-100)
REVERT: K  120 VAL cc_start: 0.7481 (t) cc_final: 0.6730 (t)
REVERT: L   50 CYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7649 (t)
  outliers start: 31
  outliers final: 20
  residues processed: 218
  average time/residue: 0.1288
  time to fit residues: 40.2100
Evaluate side-chains
  219 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.0370
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 125 optimal weight:   20.0000
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.1662

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.049250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.032749 restraints weight = 81769.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 3.03
r_work: 0.2542 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2536 r_free = 0.2536    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2536 r_free = 0.2536    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8857
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15173  Z= 0.149
  Angle     :  0.652  11.604  21790  Z= 0.377
  Chirality :  0.044   0.294   2489
  Planarity :  0.004   0.058   1746
  Dihedral  : 29.888 173.386   4385
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.72 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.76 (0.27), residues: 1033
  helix:  2.23 (0.21), residues: 655
  sheet: -1.07 (0.93), residues: 24
  loop : -0.74 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K 125 
 TYR   0.042   0.002   TYR D  83 
 PHE   0.013   0.002   PHE A  67 
 TRP   0.007   0.001   TRP L  61 
 HIS   0.003   0.001   HIS K  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.15 (15165)
  covalent geometry    : angle       0.64985 /  0.38 (21781)
  hydrogen bonds       : bond        0.08871 /  6.03 (  827)
  hydrogen bonds       : angle       3.41818 /  2.50 ( 2029)
  metal coordination   : bond        0.00503 /  0.21 (    8)
  metal coordination   : angle       2.87464 /  1.50 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 220
  time to evaluate  : 0.392 
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: A   59 GLU cc_start: 0.9170 (pm20) cc_final: 0.8824 (pm20)
REVERT: A   73 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9238 (tm-30)
REVERT: A   94 GLU cc_start: 0.8870 (tp30) cc_final: 0.8587 (tt0)
REVERT: B   23 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8202 (ptp90)
REVERT: C   24 GLN cc_start: 0.9313 (mm-40) cc_final: 0.8815 (mp10)
REVERT: C   56 GLU cc_start: 0.9304 (tt0) cc_final: 0.8960 (tt0)
REVERT: E   73 GLU cc_start: 0.8713 (tt0) cc_final: 0.8479 (tt0)
REVERT: E   94 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8981 (mm-30)
REVERT: F   88 TYR cc_start: 0.9007 (m-10) cc_final: 0.8696 (m-10)
REVERT: F   91 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9133 (ttpt)
REVERT: G   61 GLU cc_start: 0.9073 (tp30) cc_final: 0.8751 (tp30)
REVERT: G   64 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.9005 (pp20)
REVERT: D   93 GLU cc_start: 0.8875 (mp0) cc_final: 0.8657 (mp0)
REVERT: H   33 ARG cc_start: 0.8418 (mtp85) cc_final: 0.7702 (ttp-110)
REVERT: H   51 ASP cc_start: 0.8665 (p0) cc_final: 0.8463 (p0)
REVERT: H   83 TYR cc_start: 0.8592 (m-10) cc_final: 0.8138 (m-10)
REVERT: H  105 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: H  106 LEU cc_start: 0.9410 (mt) cc_final: 0.9142 (mt)
REVERT: H  113 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8988 (mm-30)
REVERT: K    1 MET cc_start: 0.7493 (tmm) cc_final: 0.7155 (tmm)
REVERT: K   38 MET cc_start: 0.9119 (mtt) cc_final: 0.8696 (tpt)
REVERT: K   92 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8793 (tp-100)
REVERT: K  120 VAL cc_start: 0.7541 (t) cc_final: 0.6902 (t)
REVERT: L   50 CYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7361 (t)
REVERT: L   73 ASN cc_start: 0.7413 (t0) cc_final: 0.7175 (t0)
  outliers start: 27
  outliers final: 18
  residues processed: 232
  average time/residue: 0.1204
  time to fit residues: 40.0800
Evaluate side-chains
  227 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 206
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue   69 PHE
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   41 GLN
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 36 optimal weight:    0.0070
   chunk 80 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 58 optimal weight:   20.0000
   chunk 26 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 120 optimal weight:    0.0010
   chunk 113 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.3804

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 ASN
L  81 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.049934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.033513 restraints weight = 79591.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 2.97
r_work: 0.2572 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053  15173  Z= 0.139
  Angle     :  0.642  10.612  21790  Z= 0.370
  Chirality :  0.043   0.286   2489
  Planarity :  0.004   0.059   1746
  Dihedral  : 29.798 172.324   4381
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.42 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.84 (0.27), residues: 1033
  helix:  2.31 (0.21), residues: 648
  sheet: -0.69 (0.95), residues: 24
  loop : -0.70 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  55 
 TYR   0.036   0.001   TYR D  83 
 PHE   0.013   0.001   PHE A  67 
 TRP   0.010   0.001   TRP K 141 
 HIS   0.003   0.001   HIS L  65 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.14 (15165)
  covalent geometry    : angle       0.63966 /  0.37 (21781)
  hydrogen bonds       : bond        0.08847 /  6.00 (  827)
  hydrogen bonds       : angle       3.33073 /  2.44 ( 2029)
  metal coordination   : bond        0.00412 /  0.18 (    8)
  metal coordination   : angle       2.54305 /  1.36 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9107 (pm20) cc_final: 0.8770 (pm20)
REVERT: A   73 GLU cc_start: 0.9467 (tm-30) cc_final: 0.9218 (tm-30)
REVERT: A   94 GLU cc_start: 0.8871 (tp30) cc_final: 0.8544 (tt0)
REVERT: A   97 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8553 (mm-30)
REVERT: B   23 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8271 (ptp90)
REVERT: C   24 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8803 (mp10)
REVERT: C   56 GLU cc_start: 0.9254 (tt0) cc_final: 0.8740 (tt0)
REVERT: E   73 GLU cc_start: 0.8687 (tt0) cc_final: 0.8448 (tt0)
REVERT: F   91 LYS cc_start: 0.9440 (ttmt) cc_final: 0.9128 (ttpt)
REVERT: G   61 GLU cc_start: 0.9037 (tp30) cc_final: 0.8742 (tp30)
REVERT: G   64 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9050 (pp20)
REVERT: D   93 GLU cc_start: 0.8904 (mp0) cc_final: 0.8687 (mp0)
REVERT: H   33 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7771 (ttp-110)
REVERT: H   83 TYR cc_start: 0.8572 (m-10) cc_final: 0.8239 (m-10)
REVERT: H  105 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7733 (tm-30)
REVERT: H  106 LEU cc_start: 0.9395 (mt) cc_final: 0.9130 (mt)
REVERT: H  113 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8964 (mm-30)
REVERT: K    1 MET cc_start: 0.7499 (tmm) cc_final: 0.7170 (tmm)
REVERT: K   38 MET cc_start: 0.9078 (mtt) cc_final: 0.8681 (tpt)
REVERT: K   87 ASP cc_start: 0.8722 (p0) cc_final: 0.8509 (t0)
REVERT: K  120 VAL cc_start: 0.7408 (t) cc_final: 0.7030 (t)
REVERT: K  136 ARG cc_start: 0.9365 (ptt90) cc_final: 0.9042 (ttp-110)
REVERT: L   50 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7434 (t)
REVERT: L   73 ASN cc_start: 0.7413 (t0) cc_final: 0.7163 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 225
  average time/residue: 0.1249
  time to fit residues: 40.3697
Evaluate side-chains
  214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   69 PHE
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 65 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0040
   chunk 79 optimal weight:   20.0000
   overall best weight:    1.3798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  92 GLN
L  15 GLN
L  81 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.049550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.033148 restraints weight = 81567.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.2738 rms_B_bonded: 3.00
r_work: 0.2565 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (10 function evaluations)
r_final: 0.2560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15173  Z= 0.153
  Angle     :  0.653   9.989  21790  Z= 0.374
  Chirality :  0.043   0.278   2489
  Planarity :  0.004   0.058   1746
  Dihedral  : 29.832 172.418   4381
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.76 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.27), residues: 1033
  helix:  2.29 (0.20), residues: 654
  sheet: -0.75 (0.90), residues: 24
  loop : -0.68 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 134 
 TYR   0.060   0.002   TYR D  83 
 PHE   0.012   0.001   PHE E  67 
 TRP   0.022   0.002   TRP K 141 
 HIS   0.005   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 (15165)
  covalent geometry    : angle       0.65043 /  0.37 (21781)
  hydrogen bonds       : bond        0.08684 /  5.89 (  827)
  hydrogen bonds       : angle       3.38312 /  2.48 ( 2029)
  metal coordination   : bond        0.00783 /  0.37 (    8)
  metal coordination   : angle       2.95569 /  1.51 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9143 (pm20) cc_final: 0.8783 (pm20)
REVERT: A   73 GLU cc_start: 0.9474 (tm-30) cc_final: 0.9179 (tm-30)
REVERT: A   94 GLU cc_start: 0.8849 (tp30) cc_final: 0.8515 (tt0)
REVERT: B   23 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8184 (ptp90)
REVERT: C   24 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8779 (mp10)
REVERT: C   56 GLU cc_start: 0.9308 (tt0) cc_final: 0.8751 (tt0)
REVERT: F   91 LYS cc_start: 0.9458 (ttmt) cc_final: 0.9137 (ttpt)
REVERT: G   61 GLU cc_start: 0.9064 (tp30) cc_final: 0.8770 (tp30)
REVERT: G   64 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9068 (pp20)
REVERT: D   83 TYR cc_start: 0.8144 (m-80) cc_final: 0.7897 (m-80)
REVERT: D   93 GLU cc_start: 0.8929 (mp0) cc_final: 0.8695 (mp0)
REVERT: H   33 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7943 (mtm180)
REVERT: H   83 TYR cc_start: 0.8578 (m-10) cc_final: 0.8266 (m-10)
REVERT: H  105 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: H  106 LEU cc_start: 0.9403 (mt) cc_final: 0.9134 (mt)
REVERT: H  113 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9062 (mm-30)
REVERT: K    1 MET cc_start: 0.7494 (tmm) cc_final: 0.7171 (tmm)
REVERT: K   38 MET cc_start: 0.9073 (mtt) cc_final: 0.8699 (tpt)
REVERT: K   41 ASN cc_start: 0.8686 (m-40) cc_final: 0.8437 (p0)
REVERT: K   87 ASP cc_start: 0.8788 (p0) cc_final: 0.8547 (t0)
REVERT: K  120 VAL cc_start: 0.7527 (t) cc_final: 0.7068 (t)
REVERT: K  136 ARG cc_start: 0.9355 (ptt90) cc_final: 0.9093 (ttp-110)
REVERT: K  147 MET cc_start: 0.8607 (mtt) cc_final: 0.8078 (mpp)
REVERT: L   73 ASN cc_start: 0.7419 (t0) cc_final: 0.7194 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 218
  average time/residue: 0.1197
  time to fit residues: 37.6771
Evaluate side-chains
  212 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 197
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   69 PHE
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 81 optimal weight:   20.0000
   chunk 3 optimal weight:    0.3980
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.049767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.033395 restraints weight = 81692.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 2.99
r_work: 0.2569 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15173  Z= 0.147
  Angle     :  0.650   9.424  21790  Z= 0.371
  Chirality :  0.042   0.277   2489
  Planarity :  0.004   0.059   1746
  Dihedral  : 29.842 172.455   4381
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.80 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.27), residues: 1033
  helix:  2.35 (0.21), residues: 648
  sheet: -0.78 (0.92), residues: 24
  loop : -0.63 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 125 
 TYR   0.055   0.002   TYR D  83 
 PHE   0.012   0.001   PHE E  67 
 TRP   0.009   0.001   TRP K 141 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.15 (15165)
  covalent geometry    : angle       0.64724 /  0.37 (21781)
  hydrogen bonds       : bond        0.08592 /  5.83 (  827)
  hydrogen bonds       : angle       3.31819 /  2.44 ( 2029)
  metal coordination   : bond        0.00648 /  0.29 (    8)
  metal coordination   : angle       3.17049 /  1.75 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 211
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9117 (pm20) cc_final: 0.8773 (pm20)
REVERT: A   73 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9154 (tm-30)
REVERT: A   94 GLU cc_start: 0.8835 (tp30) cc_final: 0.8592 (tt0)
REVERT: C   24 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8788 (mp10)
REVERT: C   56 GLU cc_start: 0.9287 (tt0) cc_final: 0.8739 (tt0)
REVERT: E   73 GLU cc_start: 0.8743 (tt0) cc_final: 0.8542 (tt0)
REVERT: F   91 LYS cc_start: 0.9446 (ttmt) cc_final: 0.9126 (ttpt)
REVERT: G   61 GLU cc_start: 0.9020 (tp30) cc_final: 0.8773 (tp30)
REVERT: G   64 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9074 (pp20)
REVERT: H   33 ARG cc_start: 0.8334 (mtp85) cc_final: 0.7785 (ttp-110)
REVERT: H   83 TYR cc_start: 0.8575 (m-10) cc_final: 0.8315 (m-10)
REVERT: H  105 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7715 (tm-30)
REVERT: H  106 LEU cc_start: 0.9398 (mt) cc_final: 0.9122 (mt)
REVERT: H  113 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8900 (mt-10)
REVERT: K    1 MET cc_start: 0.7496 (tmm) cc_final: 0.7176 (tmm)
REVERT: K   38 MET cc_start: 0.9116 (mtt) cc_final: 0.8711 (tpt)
REVERT: K   41 ASN cc_start: 0.8623 (m-40) cc_final: 0.8374 (p0)
REVERT: K   87 ASP cc_start: 0.8811 (p0) cc_final: 0.8561 (t0)
REVERT: K  120 VAL cc_start: 0.7449 (t) cc_final: 0.7232 (t)
REVERT: K  136 ARG cc_start: 0.9381 (ptt90) cc_final: 0.9125 (ttp-110)
REVERT: L   73 ASN cc_start: 0.7467 (t0) cc_final: 0.7237 (t0)
  outliers start: 15
  outliers final: 14
  residues processed: 220
  average time/residue: 0.1236
  time to fit residues: 39.3700
Evaluate side-chains
  217 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 107 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 71 optimal weight:   20.0000
   chunk 113 optimal weight:    6.9990
   chunk 121 optimal weight:    0.7980
   chunk 119 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   overall best weight:    2.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
E 113 HIS
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 143 GLN
L  81 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.049271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.032889 restraints weight = 81797.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 2.99
r_work: 0.2554 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2547 r_free = 0.2547    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2547 r_free = 0.2547    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15173  Z= 0.186
  Angle     :  0.677  13.033  21790  Z= 0.381
  Chirality :  0.043   0.270   2489
  Planarity :  0.004   0.057   1746
  Dihedral  : 29.931 172.887   4381
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.03 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.27), residues: 1033
  helix:  2.33 (0.21), residues: 648
  sheet: -0.81 (0.92), residues: 24
  loop : -0.59 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 134 
 TYR   0.078   0.002   TYR D  83 
 PHE   0.013   0.001   PHE E  67 
 TRP   0.038   0.003   TRP K  93 
 HIS   0.005   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.19 (15165)
  covalent geometry    : angle       0.67471 /  0.38 (21781)
  hydrogen bonds       : bond        0.08490 /  5.76 (  827)
  hydrogen bonds       : angle       3.39629 /  2.48 ( 2029)
  metal coordination   : bond        0.00652 /  0.29 (    8)
  metal coordination   : angle       3.05311 /  1.75 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 201
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9125 (pm20) cc_final: 0.8789 (pm20)
REVERT: A   73 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9151 (tm-30)
REVERT: A   94 GLU cc_start: 0.8840 (tp30) cc_final: 0.8507 (tt0)
REVERT: C   24 GLN cc_start: 0.9351 (mm-40) cc_final: 0.8794 (mp10)
REVERT: C   56 GLU cc_start: 0.9296 (tt0) cc_final: 0.8728 (tt0)
REVERT: C   95 LYS cc_start: 0.9664 (tptt) cc_final: 0.9453 (tptp)
REVERT: E   73 GLU cc_start: 0.8660 (tt0) cc_final: 0.8439 (tt0)
REVERT: F   91 LYS cc_start: 0.9456 (ttmt) cc_final: 0.9122 (ttpt)
REVERT: G   61 GLU cc_start: 0.9053 (tp30) cc_final: 0.8766 (tp30)
REVERT: G   64 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9116 (pp20)
REVERT: D   93 GLU cc_start: 0.8827 (mp0) cc_final: 0.8540 (mp0)
REVERT: H   33 ARG cc_start: 0.8354 (mtp85) cc_final: 0.7829 (ttp-110)
REVERT: H   83 TYR cc_start: 0.8580 (m-10) cc_final: 0.8266 (m-10)
REVERT: H  105 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7739 (tm-30)
REVERT: H  106 LEU cc_start: 0.9439 (mt) cc_final: 0.9176 (mt)
REVERT: H  113 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8909 (mt-10)
REVERT: K    1 MET cc_start: 0.7504 (tmm) cc_final: 0.7174 (tmm)
REVERT: K   38 MET cc_start: 0.9129 (mtt) cc_final: 0.8703 (tpt)
REVERT: K   87 ASP cc_start: 0.8802 (p0) cc_final: 0.8577 (t0)
REVERT: K  120 VAL cc_start: 0.7450 (OUTLIER) cc_final: 0.7180 (t)
REVERT: K  136 ARG cc_start: 0.9398 (ptt90) cc_final: 0.9137 (ttp-110)
REVERT: L   73 ASN cc_start: 0.7394 (t0) cc_final: 0.7129 (m110)
  outliers start: 19
  outliers final: 17
  residues processed: 211
  average time/residue: 0.1194
  time to fit residues: 36.5463
Evaluate side-chains
  213 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 194
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue  120 VAL
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain K residue  143 GLN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 102 optimal weight:   30.0000
   chunk 105 optimal weight:    0.8980
   chunk 127 optimal weight:   40.0000
   chunk 1 optimal weight:    0.9990
   chunk 112 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 120 optimal weight:    4.9990
   chunk 111 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
G  38 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 143 GLN
L  81 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.049871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.033582 restraints weight = 81273.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 2.98
r_work: 0.2581 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (10 function evaluations)
r_final: 0.2573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15173  Z= 0.141
  Angle     :  0.658  12.104  21790  Z= 0.375
  Chirality :  0.042   0.277   2489
  Planarity :  0.004   0.060   1746
  Dihedral  : 29.877 172.595   4381
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.61 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.27), residues: 1033
  helix:  2.30 (0.21), residues: 649
  sheet: -0.71 (0.94), residues: 24
  loop : -0.58 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 134 
 TYR   0.078   0.002   TYR D  83 
 PHE   0.012   0.001   PHE E  67 
 TRP   0.032   0.002   TRP K  93 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.14 (15165)
  covalent geometry    : angle       0.65588 /  0.37 (21781)
  hydrogen bonds       : bond        0.08556 /  5.79 (  827)
  hydrogen bonds       : angle       3.29674 /  2.41 ( 2029)
  metal coordination   : bond        0.00470 /  0.21 (    8)
  metal coordination   : angle       2.72395 /  1.51 (    9)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.337 
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   59 GLU cc_start: 0.9091 (pm20) cc_final: 0.8724 (pm20)
REVERT: A   73 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9165 (tm-30)
REVERT: A   94 GLU cc_start: 0.8854 (tp30) cc_final: 0.8504 (tt0)
REVERT: C   24 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8770 (mp10)
REVERT: C   56 GLU cc_start: 0.9317 (tt0) cc_final: 0.8727 (tt0)
REVERT: C   95 LYS cc_start: 0.9664 (tptt) cc_final: 0.9450 (tptp)
REVERT: E   73 GLU cc_start: 0.8724 (tt0) cc_final: 0.8477 (tt0)
REVERT: F   91 LYS cc_start: 0.9465 (ttmt) cc_final: 0.9144 (ttpt)
REVERT: G   61 GLU cc_start: 0.9005 (tp30) cc_final: 0.8755 (tp30)
REVERT: G   64 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.9083 (pp20)
REVERT: D   93 GLU cc_start: 0.8882 (mp0) cc_final: 0.8603 (mp0)
REVERT: H   33 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7771 (ttp-110)
REVERT: H   51 ASP cc_start: 0.8715 (p0) cc_final: 0.8479 (p0)
REVERT: H   83 TYR cc_start: 0.8563 (m-10) cc_final: 0.8311 (m-10)
REVERT: H  105 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7713 (tm-30)
REVERT: H  106 LEU cc_start: 0.9396 (mt) cc_final: 0.9128 (mt)
REVERT: H  113 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8913 (mt-10)
REVERT: K    1 MET cc_start: 0.7513 (tmm) cc_final: 0.7196 (tmm)
REVERT: K   38 MET cc_start: 0.9100 (mtt) cc_final: 0.8684 (tpt)
REVERT: K   87 ASP cc_start: 0.8823 (p0) cc_final: 0.8574 (t0)
REVERT: K  120 VAL cc_start: 0.7350 (OUTLIER) cc_final: 0.7109 (t)
REVERT: K  136 ARG cc_start: 0.9396 (ptt90) cc_final: 0.9069 (ttp-110)
  outliers start: 20
  outliers final: 18
  residues processed: 214
  average time/residue: 0.1192
  time to fit residues: 36.9411
Evaluate side-chains
  220 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue  120 VAL
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain K residue  143 GLN
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 122 optimal weight:    1.9990
   chunk 126 optimal weight:    7.9990
   chunk 127 optimal weight:   30.0000
   chunk 72 optimal weight:   20.0000
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
G  38 ASN
L  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.049844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.033552 restraints weight = 81570.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 2.98
r_work: 0.2579 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (11 function evaluations)
r_final: 0.2573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.137  15173  Z= 0.200
  Angle     :  0.960  59.187  21790  Z= 0.583
  Chirality :  0.045   0.698   2489
  Planarity :  0.005   0.060   1746
  Dihedral  : 29.877 172.579   4381
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.19 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.95 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.27), residues: 1033
  helix:  2.25 (0.21), residues: 650
  sheet: -0.72 (0.94), residues: 24
  loop : -0.57 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 134 
 TYR   0.081   0.003   TYR B  88 
 PHE   0.012   0.001   PHE E  67 
 TRP   0.027   0.002   TRP K  93 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.20 (15165)
  covalent geometry    : angle       0.95845 /  0.58 (21781)
  hydrogen bonds       : bond        0.08556 /  5.79 (  827)
  hydrogen bonds       : angle       3.29297 /  2.41 ( 2029)
  metal coordination   : bond        0.00457 /  0.21 (    8)
  metal coordination   : angle       2.71673 /  1.51 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3654.11 seconds
wall clock time: 63 minutes 3.86 seconds (3783.86 seconds total)