Starting phenix.real_space_refine
on Fri Aug  7 17:51:12 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8grm_34207/08_2026/8grm_34207.cif"
  }
  resolution = 3.05
  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 10341 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      4      6.06       5
     P     289      5.49       5
     S      38      5.16       5
     C    8805      2.51       5
     N    2856      2.21       5
     O    3423      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 15415
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 800
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 652
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 753
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 795
          Classifications: {'peptide': 97}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          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: "F"
      Number of atoms: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 682
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "G"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "M"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 803
          Classifications: {'peptide': 101}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "N"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 799
          Classifications: {'peptide': 101}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 2935
          Classifications: {'DNA': 144}
          Link IDs: {'rna3p': 143}
    Chain: "J"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "O"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 601
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "P"
      Number of atoms: 1169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1169
          Classifications: {'peptide': 146}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 130}
    Chain: "M"
      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}
    Chain: "N"
      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   6391  SG  CYS M  39      41.225  89.870  60.488  1.00 36.05           S
  ATOM   6413  SG  CYS M  42      37.771  87.794  58.649  1.00 38.01           S
  ATOM   6350  SG  CYS M  34      45.303  77.408  52.391  1.00 28.86           S
  ATOM   6508  SG  CYS M  53      42.351  79.379  51.567  1.00 36.39           S
  ATOM   6529  SG  CYS M  56      44.443  77.373  48.319  1.00 36.87           S
  ATOM   7206  SG  CYS N  51      67.205  82.068  57.667  1.00 35.68           S
  ATOM   7227  SG  CYS N  54      70.266  83.831  55.992  1.00 38.12           S
  ATOM   7375  SG  CYS N  72      66.888  82.641  53.908  1.00 30.84           S
  ATOM   7394  SG  CYS N  75      69.602  79.730  55.415  1.00 30.00           S
  ATOM   7329  SG  CYS N  67      56.883  74.476  65.266  1.00 24.81           S
  ATOM   7483  SG  CYS N  87      60.911  75.821  64.242  1.00 27.17           S
  ATOM   7503  SG  CYS N  90      58.841  77.321  67.718  1.00 32.49           S

  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   GLY O  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY O  75 " occ=0.25
    residue:
      pdb=" N   GLY O  76 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY O  76 " occ=0.25
  Time building chain proxies: 3.20, per 1000 atoms: 0.21
  Number of scatterers: 15415
  At special positions: 0
  Unit cell: (117.066, 117.066, 123.51, 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      4     29.99
     S      38     16.00
     P     289     15.00
     O    3423      8.00
     N    2856      7.00
     C    8805      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: 1.03
  Conformation dependent library (CDL) restraints added in 529.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN M 201 "
        pdb="ZN    ZN M 201 " - pdb=" SG  CYS M  39 "
        pdb="ZN    ZN M 201 " - pdb=" SG  CYS M  42 "
      pdb="  ZN M 202 "
        pdb="ZN    ZN M 202 " - pdb=" ND1 HIS M  36 "
        pdb="ZN    ZN M 202 " - pdb=" SG  CYS M  34 "
        pdb="ZN    ZN M 202 " - pdb=" SG  CYS M  56 "
        pdb="ZN    ZN M 202 " - pdb=" SG  CYS M  53 "
      pdb="  ZN N 401 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  54 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  75 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  51 "
        pdb="ZN    ZN N 401 " - pdb=" SG  CYS N  72 "
      pdb="  ZN N 402 "
        pdb="ZN    ZN N 402 " - pdb=" SG  CYS N  87 "
        pdb="ZN    ZN N 402 " - pdb=" SG  CYS N  90 "
        pdb="ZN    ZN N 402 " - pdb=" ND1 HIS N  69 "
        pdb="ZN    ZN N 402 " - pdb=" SG  CYS N  67 "
      Number of angles added : 12


  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2252

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 17 sheets defined
      52.6% alpha, 5.7% beta
      128 base pairs and 268 stacking pairs defined.
    Time for finding SS restraints: 2.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.737A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.566A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.757A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.702A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 4.489A  pdb=" N   GLU C  61 " --> pdb=" O   TYR C  57 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 88
      removed outlier: 3.534A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN C  84 " --> pdb=" O   PRO C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.637A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.658A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL D  66 " --> pdb=" O   MET D  62 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ARG D  72 " --> pdb=" O   ASP D  68 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.511A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 119
      removed outlier: 3.718A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ALA D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 64 through 75
      removed outlier: 3.584A  pdb=" N   ARG E  69 " --> pdb=" O   LEU E  65 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU E  70 " --> pdb=" O   PRO E  66 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL E  71 " --> pdb=" O   PHE E  67 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 78
      No H-bonds generated for 'chain 'E' and resid 76 through 78'
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.511A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU E 103 " --> pdb=" O   TYR E  99 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS E 110 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 4.048A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 74
      removed outlier: 3.770A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.667A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 4.489A  pdb=" N   GLU G  61 " --> pdb=" O   TYR G  57 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 88
      removed outlier: 3.534A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN G  84 " --> pdb=" O   PRO G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.539A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.762A  pdb=" N   ILE H  61 " --> pdb=" O   LYS H  57 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER H  64 " --> pdb=" O   GLY H  60 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLU H  71 " --> pdb=" O   ASN H  67 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ARG H  72 " --> pdb=" O   ASP H  68 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA H  81 " --> pdb=" O   ALA H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 91 through 102
      removed outlier: 3.788A  pdb=" N   THR H  96 " --> pdb=" O   ARG H  92 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA H  97 " --> pdb=" O   GLU H  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 122
      removed outlier: 3.807A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ALA H 117 " --> pdb=" O   GLU H 113 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 40 through 47
      removed outlier: 4.626A  pdb=" N   ARG M  45 " --> pdb=" O   THR M  41 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 72 through 83
      removed outlier: 3.782A  pdb=" N   GLN M  76 " --> pdb=" O   ASP M  72 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS M  81 " --> pdb=" O   ASP M  77 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 86 through 99
      removed outlier: 3.636A  pdb=" N   MET M  91 " --> pdb=" O   PHE M  87 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 20 through 25
    Processing helix  chain 'N' and resid 45 through 50
      removed outlier: 3.787A  pdb=" N   LEU N  49 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET N  50 " --> pdb=" O   HIS N  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 45 through 50'
    Processing helix  chain 'N' and resid 73 through 82
      removed outlier: 3.555A  pdb=" N   ILE N  77 " --> pdb=" O   ALA N  73 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  74 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 96 through 98
      No H-bonds generated for 'chain 'N' and resid 96 through 98'
    Processing helix  chain 'N' and resid 103 through 114
      removed outlier: 4.536A  pdb=" N   LEU N 109 " --> pdb=" O   ASN N 105 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE N 110 " --> pdb=" O   PHE N 106 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 22 through 35
      removed outlier: 3.610A  pdb=" N   ILE O  30 " --> pdb=" O   VAL O  26 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASP O  32 " --> pdb=" O   ALA O  28 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS O  33 " --> pdb=" O   LYS O  29 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 37 through 39
      No H-bonds generated for 'chain 'O' and resid 37 through 39'
    Processing helix  chain 'P' and resid 3 through 15
      removed outlier: 3.736A  pdb=" N   HIS P   7 " --> pdb=" O   LEU P   3 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS P   8 " --> pdb=" O   LYS P   4 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 98 through 108
      removed outlier: 3.961A  pdb=" N   LEU P 104 " --> pdb=" O   SER P 100 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 123 through 128
      removed outlier: 4.033A  pdb=" N   TYR P 127 " --> pdb=" O   ILE P 123 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS P 128 " --> pdb=" O   ALA P 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 123 through 128'
    Processing helix  chain 'P' and resid 133 through 141
      removed outlier: 4.058A  pdb=" N   ARG P 139 " --> pdb=" O   ASN P 135 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.885A  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 96 through 98
      removed outlier: 6.400A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.135A  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
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.032A  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: 7.196A  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 'M' and resid 7 through 8
    Processing sheet with id=AB3, first strand: chain 'M' and resid 37 through 39
    Processing sheet with id=AB4, first strand: chain 'N' and resid 70 through 72
    Processing sheet with id=AB5, first strand: chain 'O' and resid 13 through 16
      removed outlier: 3.584A  pdb=" N   LEU O  15 " --> pdb=" O   ILE O   3 " (cutoff:3.500A)
      removed outlier: 9.055A  pdb=" N   LEU O  67 " --> pdb=" O   GLN O   2 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   PHE O   4 " --> pdb=" O   LEU O  67 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'O' and resid 41 through 42
      removed outlier: 3.603A  pdb=" N   VAL O  70 " --> pdb=" O   ARG O  42 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'O' and resid 44 through 45
    Processing sheet with id=AB8, first strand: chain 'P' and resid 21 through 25
      removed outlier: 3.501A  pdb=" N   SER P  22 " --> pdb=" O   THR P  36 " (cutoff:3.500A)

    408 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      317 hydrogen bonds
      630 hydrogen bond angles
      0 basepair planarities
      128 basepair parallelities
      268 stacking parallelities
  Total time for adding SS restraints: 2.69

  Time building geometry restraints manager: 1.48 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: 3139
        1.33 -     1.45: 4865
        1.45 -     1.57: 7649
        1.57 -     1.69: 576
        1.69 -     1.81: 57
  Bond restraints: 16286
  Sorted by residual:
  bond pdb=" C   LEU E  65 "
       pdb=" N   PRO E  66 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.043 8.40e-03 1.42e+04 2.58e+01
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.435  1.494 -0.059 1.30e-02 5.92e+03 2.03e+01
  bond pdb=" C1'  DC I -71 "
       pdb=" N1   DC I -71 "
    ideal  model  delta    sigma   weight residual
    1.468  1.528 -0.060 1.40e-02 5.10e+03 1.85e+01
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.435  1.488 -0.053 1.30e-02 5.92e+03 1.68e+01
  bond pdb=" CG1 ILE B  50 "
       pdb=" CD1 ILE B  50 "
    ideal  model  delta    sigma   weight residual
    1.513  1.367  0.146 3.90e-02 6.57e+02 1.40e+01
  ... (remaining 16281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 22485
        2.42 -     4.85: 659
        4.85 -     7.27: 77
        7.27 -     9.69: 12
        9.69 -    12.12: 7
  Bond angle restraints: 23240
  Sorted by residual:
  angle pdb=" C   LYS C  15 "
        pdb=" N   THR C  16 "
        pdb=" CA  THR C  16 "
      ideal   model   delta    sigma   weight residual
     121.54  133.14  -11.60 1.91e+00 2.74e-01 3.69e+01
  angle pdb=" C   LYS G  15 "
        pdb=" N   THR G  16 "
        pdb=" CA  THR G  16 "
      ideal   model   delta    sigma   weight residual
     121.54  133.09  -11.55 1.91e+00 2.74e-01 3.66e+01
  angle pdb=" C3'  DG J  20 "
        pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
      ideal   model   delta    sigma   weight residual
     119.70  125.66   -5.96 1.20e+00 6.94e-01 2.47e+01
  angle pdb=" CB  ARG M  70 "
        pdb=" CG  ARG M  70 "
        pdb=" CD  ARG M  70 "
      ideal   model   delta    sigma   weight residual
     111.30  122.60  -11.30 2.30e+00 1.89e-01 2.41e+01
  angle pdb=" C3'  DT J -17 "
        pdb=" O3'  DT J -17 "
        pdb=" P    DT J -16 "
      ideal   model   delta    sigma   weight residual
     119.70  125.47   -5.77 1.20e+00 6.94e-01 2.31e+01
  ... (remaining 23235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.42: 7860
       35.42 -    70.83: 1255
       70.83 -   106.25: 1
      106.25 -   141.67: 0
      141.67 -   177.09: 2
  Dihedral angle restraints: 9118
    sinusoidal: 5639
      harmonic: 3479
  Sorted by residual:
  dihedral pdb=" CA  GLY P  48 "
           pdb=" C   GLY P  48 "
           pdb=" N   VAL P  49 "
           pdb=" CA  VAL P  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -134.44  -45.56     0      5.00e+00 4.00e-02 8.30e+01
  dihedral pdb=" CA  ARG B  39 "
           pdb=" C   ARG B  39 "
           pdb=" N   ARG B  40 "
           pdb=" CA  ARG B  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.13   30.87     0      5.00e+00 4.00e-02 3.81e+01
  dihedral pdb=" CA  ILE H  69 "
           pdb=" C   ILE H  69 "
           pdb=" N   PHE H  70 "
           pdb=" CA  PHE H  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.72   30.28     0      5.00e+00 4.00e-02 3.67e+01
  ... (remaining 9115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.123: 2536
       0.123 -    0.246: 101
       0.246 -    0.368: 6
       0.368 -    0.491: 0
       0.491 -    0.614: 1
  Chirality restraints: 2644
  Sorted by residual:
  chirality pdb=" CB  ILE E  62 "
            pdb=" CA  ILE E  62 "
            pdb=" CG1 ILE E  62 "
            pdb=" CG2 ILE E  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.03    0.61 2.00e-01 2.50e+01 9.42e+00
  chirality pdb=" CB  THR A 118 "
            pdb=" CA  THR A 118 "
            pdb=" OG1 THR A 118 "
            pdb=" CG2 THR A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.21    0.34 2.00e-01 2.50e+01 2.92e+00
  chirality pdb=" CB  THR C  16 "
            pdb=" CA  THR C  16 "
            pdb=" OG1 THR C  16 "
            pdb=" CG2 THR C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.24    0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 2641 not shown)

  Planarity restraints: 1942
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  98 "   -0.002 2.00e-02 2.50e+03   2.26e-02 1.02e+01
        pdb=" CG  TYR F  98 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  98 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  98 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  98 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  98 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  98 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR F  98 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY P  48 "    0.013 2.00e-02 2.50e+03   2.54e-02 6.43e+00
        pdb=" C   GLY P  48 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   GLY P  48 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL P  49 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C  13 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.68e+00
        pdb=" C   LYS C  13 "    0.041 2.00e-02 2.50e+03
        pdb=" O   LYS C  13 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA C  14 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1939 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3654
        2.81 -     3.33: 11961
        3.33 -     3.86: 27397
        3.86 -     4.38: 35337
        4.38 -     4.90: 50424
  Nonbonded interactions: 128773
  Sorted by model distance:
  nonbonded pdb=" OG  SER P  22 "
            pdb=" OG1 THR P  36 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ILE N  53 "
            pdb=" NH1 ARG P   5 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" NH1 ARG D  31 "
            pdb=" OP1  DG J  51 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OH  TYR M  80 "
            pdb=" OE1 GLU M  90 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" NH2 ARG G  29 "
            pdb=" OP1  DC I  49 "
     model   vdw
     2.349 3.120
  ... (remaining 128768 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'
  selection = (chain 'F' and resid 21 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 31 through 125)
  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=0.25 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.600
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.050
  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:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
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      :  0.013   0.817  16300  Z= 0.713
  Angle     :  1.041  15.625  23252  Z= 0.724
  Chirality :  0.063   0.614   2644
  Planarity :  0.006   0.057   1942
  Dihedral  : 23.197 177.086   6866
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  1.27 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -5.38 (0.17), residues: 1171
  helix: -4.45 (0.09), residues: 631
  sheet: -1.78 (0.72), residues: 53
  loop : -2.25 (0.23), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG P   5 
 TYR   0.048   0.004   TYR F  98 
 PHE   0.041   0.005   PHE F  61 
 TRP   0.027   0.003   TRP P  33 
 HIS   0.011   0.003   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00950 /  0.66 (16286)
  covalent geometry    : angle       1.02279 /  0.72 (23240)
  hydrogen bonds       : bond        0.29765 / 19.89 (  725)
  hydrogen bonds       : angle      10.28662 /  7.30 ( 1833)
  metal coordination   : bond        0.31899 / 22.63 (   14)
  metal coordination   : angle       8.48797 /  4.84 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 367
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6716 (mt-10)
REVERT: A  106 ASP cc_start: 0.8163 (m-30) cc_final: 0.7762 (m-30)
REVERT: D   63 ASN cc_start: 0.7781 (m-40) cc_final: 0.7544 (m110)
REVERT: E   58 THR cc_start: 0.8968 (p) cc_final: 0.8751 (p)
REVERT: N   22 TYR cc_start: 0.7669 (t80) cc_final: 0.7379 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 369
  average time/residue: 0.2061
  time to fit residues: 97.8700
Evaluate side-chains
  266 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 ASN
B  27 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
C  82 HIS
C 112 GLN
D  47 GLN
D  82 HIS
E 108 ASN
F  25 ASN
F  93 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  82 HIS
G  94 ASN
M  76 GLN
O  25 ASN
O  31 GLN
P  77 ASN
P  79 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.139443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.100440 restraints weight = 22387.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.84
r_work: 0.3021 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (10 function evaluations)
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
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   0.063  16300  Z= 0.188
  Angle     :  0.818   8.547  23252  Z= 0.445
  Chirality :  0.054   0.321   2644
  Planarity :  0.006   0.068   1942
  Dihedral  : 28.768 175.432   4475
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 10.86 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.26 (0.20), residues: 1171
  helix: -2.27 (0.16), residues: 649
  sheet: -1.05 (0.65), residues: 68
  loop : -1.91 (0.25), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  53 
 TYR   0.019   0.002   TYR E  99 
 PHE   0.029   0.003   PHE P  50 
 TRP   0.005   0.001   TRP P  33 
 HIS   0.012   0.002   HIS P  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.19 (16286)
  covalent geometry    : angle       0.81662 /  0.45 (23240)
  hydrogen bonds       : bond        0.06345 /  4.22 (  725)
  hydrogen bonds       : angle       3.99759 /  2.81 ( 1833)
  metal coordination   : bond        0.01535 /  1.06 (   14)
  metal coordination   : angle       2.31616 /  1.26 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 291
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: B   59 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8483 (tptt)
REVERT: B   97 LEU cc_start: 0.9346 (mt) cc_final: 0.9061 (tp)
REVERT: C   17 ARG cc_start: 0.8382 (mtt180) cc_final: 0.8131 (mtm180)
REVERT: C   56 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8400 (tt0)
REVERT: C   73 ASN cc_start: 0.8662 (m110) cc_final: 0.8452 (m-40)
REVERT: D  108 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8518 (mttp)
REVERT: E   58 THR cc_start: 0.9265 (p) cc_final: 0.9052 (p)
REVERT: E  129 ARG cc_start: 0.8897 (ttm170) cc_final: 0.8542 (tpt90)
REVERT: H  105 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8024 (tt0)
REVERT: M   11 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7447 (pm20)
REVERT: M   64 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.9200 (mtp180)
REVERT: O    1 MET cc_start: 0.6614 (pmm) cc_final: 0.6322 (pmm)
REVERT: P  105 SER cc_start: 0.9048 (t) cc_final: 0.8613 (p)
  outliers start: 30
  outliers final: 17
  residues processed: 302
  average time/residue: 0.1720
  time to fit residues: 70.6934
Evaluate side-chains
  279 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 259
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain M residue    9 ILE
Chi-restraints excluded: chain M residue   11 GLU
Chi-restraints excluded: chain M residue   29 THR
Chi-restraints excluded: chain M residue   64 ARG
Chi-restraints excluded: chain N residue   21 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   67 CYS
Chi-restraints excluded: chain P residue   36 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 45 optimal weight:    0.2980
   chunk 43 optimal weight:    0.2980
   chunk 88 optimal weight:    0.5980
   chunk 111 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 77 optimal weight:    0.1980
   chunk 107 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
C  73 ASN
D  47 GLN
D  63 ASN
D  82 HIS
E  76 GLN
F  75 HIS
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
G 112 GLN
H  84 ASN
M  15 HIS
M  76 GLN
P  32 HIS
P  79 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.100346 restraints weight = 22450.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.82
r_work: 0.3023 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090  16300  Z= 0.140
  Angle     :  0.660   7.736  23252  Z= 0.374
  Chirality :  0.047   0.285   2644
  Planarity :  0.005   0.040   1942
  Dihedral  : 28.965 172.669   4475
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 11.74 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.23), residues: 1171
  helix: -1.01 (0.19), residues: 652
  sheet: -1.00 (0.70), residues: 58
  loop : -1.73 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG M  70 
 TYR   0.027   0.002   TYR P 134 
 PHE   0.031   0.002   PHE P  50 
 TRP   0.006   0.001   TRP P  33 
 HIS   0.008   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.14 (16286)
  covalent geometry    : angle       0.65826 /  0.37 (23240)
  hydrogen bonds       : bond        0.05350 /  3.54 (  725)
  hydrogen bonds       : angle       3.51293 /  2.46 ( 1833)
  metal coordination   : bond        0.02532 /  1.97 (   14)
  metal coordination   : angle       2.32661 /  1.36 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 288
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8244 (mt-10)
REVERT: A  115 LYS cc_start: 0.9081 (mttm) cc_final: 0.8801 (mmtm)
REVERT: B   59 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8506 (tptt)
REVERT: B   97 LEU cc_start: 0.9350 (mt) cc_final: 0.9131 (tp)
REVERT: C   17 ARG cc_start: 0.8398 (mtt180) cc_final: 0.8178 (mtm180)
REVERT: C   24 GLN cc_start: 0.8469 (mt0) cc_final: 0.7987 (mt0)
REVERT: C   56 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8391 (tt0)
REVERT: D   47 GLN cc_start: 0.9017 (mt0) cc_final: 0.8802 (mt0)
REVERT: E   58 THR cc_start: 0.9373 (p) cc_final: 0.9124 (p)
REVERT: E  129 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8528 (tpt90)
REVERT: M   11 GLU cc_start: 0.7965 (mp0) cc_final: 0.7598 (pm20)
REVERT: M   64 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.9204 (mtp180)
REVERT: M   92 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8442 (ttmt)
REVERT: N   56 ASP cc_start: 0.8915 (t0) cc_final: 0.8706 (t0)
REVERT: N  103 ASP cc_start: 0.7602 (t0) cc_final: 0.7316 (t0)
REVERT: O    1 MET cc_start: 0.6615 (pmm) cc_final: 0.6288 (pmm)
REVERT: P   32 HIS cc_start: 0.8047 (m-70) cc_final: 0.7749 (m90)
REVERT: P  105 SER cc_start: 0.9009 (t) cc_final: 0.8494 (p)
  outliers start: 28
  outliers final: 16
  residues processed: 298
  average time/residue: 0.1577
  time to fit residues: 63.3182
Evaluate side-chains
  287 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 269
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain M residue    9 ILE
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain M residue   64 ARG
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain P residue   36 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 121 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0670
   chunk 0 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.1322

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B  75 HIS
D  63 ASN
D  82 HIS
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
H 109 HIS
P  55 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.136716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.096387 restraints weight = 22163.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.82
r_work: 0.2961 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2819
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (8 function evaluations)
r_final: 0.2819
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  16300  Z= 0.163
  Angle     :  0.663   8.356  23252  Z= 0.369
  Chirality :  0.047   0.298   2644
  Planarity :  0.005   0.042   1942
  Dihedral  : 29.105 169.798   4475
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 12.92 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.34 (0.24), residues: 1171
  helix: -0.36 (0.20), residues: 653
  sheet: -0.83 (0.72), residues: 58
  loop : -1.56 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG M  70 
 TYR   0.028   0.002   TYR N  22 
 PHE   0.027   0.002   PHE P  50 
 TRP   0.007   0.001   TRP P 141 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.16 (16286)
  covalent geometry    : angle       0.66165 /  0.37 (23240)
  hydrogen bonds       : bond        0.04826 /  3.20 (  725)
  hydrogen bonds       : angle       3.25999 /  2.28 ( 1833)
  metal coordination   : bond        0.01672 /  1.27 (   14)
  metal coordination   : angle       1.95432 /  1.22 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 270
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9119 (mttm) cc_final: 0.8835 (mmtm)
REVERT: B   59 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8618 (tppt)
REVERT: C   56 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8449 (tt0)
REVERT: C   64 GLU cc_start: 0.8199 (tt0) cc_final: 0.7989 (tt0)
REVERT: D   36 SER cc_start: 0.9400 (p) cc_final: 0.9200 (p)
REVERT: E   58 THR cc_start: 0.9484 (p) cc_final: 0.9244 (p)
REVERT: E  129 ARG cc_start: 0.8908 (ttm170) cc_final: 0.8564 (tpt90)
REVERT: G   61 GLU cc_start: 0.9050 (tp30) cc_final: 0.8673 (tp30)
REVERT: H  105 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7931 (tt0)
REVERT: M   11 GLU cc_start: 0.8032 (mp0) cc_final: 0.7620 (pm20)
REVERT: M   45 ARG cc_start: 0.9281 (tpp80) cc_final: 0.9002 (ttm-80)
REVERT: M   64 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.9196 (mtp180)
REVERT: P   30 MET cc_start: 0.8065 (mmm) cc_final: 0.7799 (mmm)
REVERT: P  105 SER cc_start: 0.8956 (t) cc_final: 0.8405 (p)
  outliers start: 35
  outliers final: 21
  residues processed: 287
  average time/residue: 0.1529
  time to fit residues: 59.8095
Evaluate side-chains
  289 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 265
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain M residue   64 ARG
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain P residue   36 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0870
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 92 optimal weight:   30.0000
   chunk 86 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0870
   chunk 119 optimal weight:   20.0000
   overall best weight:    0.4936

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
B  27 GLN
D  47 GLN
D  82 HIS
E 108 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  55 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.138060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.097990 restraints weight = 22365.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.83
r_work: 0.2989 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.071  16300  Z= 0.125
  Angle     :  0.611   7.982  23252  Z= 0.348
  Chirality :  0.045   0.285   2644
  Planarity :  0.004   0.040   1942
  Dihedral  : 28.977 169.714   4475
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 14.29 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.24), residues: 1171
  helix:  0.21 (0.21), residues: 644
  sheet: -0.62 (0.73), residues: 58
  loop : -1.40 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  86 
 TYR   0.020   0.002   TYR C  57 
 PHE   0.028   0.001   PHE P  50 
 TRP   0.004   0.001   TRP P 141 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.12 (16286)
  covalent geometry    : angle       0.60981 /  0.35 (23240)
  hydrogen bonds       : bond        0.04458 /  2.98 (  725)
  hydrogen bonds       : angle       3.14664 /  2.20 ( 1833)
  metal coordination   : bond        0.01958 /  1.54 (   14)
  metal coordination   : angle       1.93649 /  1.21 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 271
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8713 (tt0) cc_final: 0.7947 (mt-10)
REVERT: A   93 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8860 (mm-40)
REVERT: A  115 LYS cc_start: 0.9146 (mttm) cc_final: 0.8859 (mmtm)
REVERT: B   59 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8596 (tppt)
REVERT: C   24 GLN cc_start: 0.8437 (mt0) cc_final: 0.7902 (mt0)
REVERT: C   56 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8463 (tt0)
REVERT: E   53 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8534 (ttm110)
REVERT: E   58 THR cc_start: 0.9496 (p) cc_final: 0.9241 (p)
REVERT: E  108 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8886 (t0)
REVERT: E  129 ARG cc_start: 0.8876 (ttm170) cc_final: 0.8566 (tpt90)
REVERT: G   61 GLU cc_start: 0.9033 (tp30) cc_final: 0.8701 (tp30)
REVERT: G   84 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8849 (mm-40)
REVERT: H  105 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7841 (tt0)
REVERT: M   11 GLU cc_start: 0.8083 (mp0) cc_final: 0.7666 (pm20)
REVERT: M   45 ARG cc_start: 0.9267 (tpp80) cc_final: 0.9054 (ttm-80)
REVERT: M   92 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8509 (ttmt)
REVERT: N   16 THR cc_start: 0.8058 (t) cc_final: 0.7162 (p)
REVERT: P  105 SER cc_start: 0.8910 (t) cc_final: 0.8339 (p)
  outliers start: 31
  outliers final: 17
  residues processed: 288
  average time/residue: 0.1571
  time to fit residues: 61.7202
Evaluate side-chains
  280 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 258
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  108 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   84 GLN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain P residue   36 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 103 optimal weight:    9.9990
   chunk 130 optimal weight:    9.9990
   chunk 9 optimal weight:    0.5980
   chunk 137 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  82 HIS
E 108 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
H 109 HIS
P  55 HIS
P  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.137359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.096973 restraints weight = 22236.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.82
r_work: 0.2973 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  16300  Z= 0.137
  Angle     :  0.617   8.321  23252  Z= 0.349
  Chirality :  0.045   0.299   2644
  Planarity :  0.004   0.035   1942
  Dihedral  : 28.972 168.321   4475
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.77 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.25), residues: 1171
  helix:  0.47 (0.21), residues: 646
  sheet: -0.50 (0.74), residues: 58
  loop : -1.33 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  53 
 TYR   0.018   0.001   TYR H  42 
 PHE   0.029   0.001   PHE P  50 
 TRP   0.008   0.001   TRP N  17 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.14 (16286)
  covalent geometry    : angle       0.61510 /  0.35 (23240)
  hydrogen bonds       : bond        0.04394 /  2.93 (  725)
  hydrogen bonds       : angle       3.09559 /  2.17 ( 1833)
  metal coordination   : bond        0.01822 /  1.43 (   14)
  metal coordination   : angle       1.94631 /  1.25 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 263
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8792 (tt0) cc_final: 0.7889 (mt-10)
REVERT: A   93 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8836 (mm-40)
REVERT: A  115 LYS cc_start: 0.9141 (mttm) cc_final: 0.8855 (mmtm)
REVERT: B   59 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8594 (tppt)
REVERT: E   58 THR cc_start: 0.9516 (p) cc_final: 0.9263 (p)
REVERT: E  129 ARG cc_start: 0.8870 (ttm170) cc_final: 0.8571 (tpt90)
REVERT: G   61 GLU cc_start: 0.9061 (tp30) cc_final: 0.8732 (tp30)
REVERT: G   84 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8940 (tp40)
REVERT: H  105 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7983 (tt0)
REVERT: H  113 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7836 (mt-10)
REVERT: M   11 GLU cc_start: 0.8067 (mp0) cc_final: 0.7674 (pm20)
REVERT: M   45 ARG cc_start: 0.9241 (tpp80) cc_final: 0.9028 (ttm-80)
REVERT: M   92 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8500 (ttmt)
REVERT: P  105 SER cc_start: 0.8891 (t) cc_final: 0.8309 (p)
REVERT: P  106 ILE cc_start: 0.9333 (mt) cc_final: 0.9132 (pt)
  outliers start: 32
  outliers final: 22
  residues processed: 281
  average time/residue: 0.1566
  time to fit residues: 60.4810
Evaluate side-chains
  286 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 261
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   84 GLN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain P residue   36 THR
Chi-restraints excluded: chain P residue  104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 83 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 133 optimal weight:    0.6980
   chunk 116 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  82 HIS
E 108 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
H 109 HIS
** M  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.138095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.098247 restraints weight = 22169.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.78
r_work: 0.2981 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.4020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  16300  Z= 0.132
  Angle     :  0.605   8.443  23252  Z= 0.345
  Chirality :  0.045   0.303   2644
  Planarity :  0.004   0.038   1942
  Dihedral  : 28.946 169.831   4475
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.26 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.25), residues: 1171
  helix:  0.81 (0.22), residues: 645
  sheet: -0.49 (0.75), residues: 58
  loop : -1.24 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  53 
 TYR   0.016   0.001   TYR H  42 
 PHE   0.018   0.001   PHE P  50 
 TRP   0.009   0.001   TRP N  17 
 HIS   0.008   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.13 (16286)
  covalent geometry    : angle       0.60369 /  0.34 (23240)
  hydrogen bonds       : bond        0.04281 /  2.87 (  725)
  hydrogen bonds       : angle       3.02048 /  2.12 ( 1833)
  metal coordination   : bond        0.01811 /  1.42 (   14)
  metal coordination   : angle       1.88808 /  1.19 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 267
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8830 (tt0) cc_final: 0.8512 (tt0)
REVERT: A   93 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8789 (mm-40)
REVERT: A  115 LYS cc_start: 0.9127 (mttm) cc_final: 0.8853 (mmtm)
REVERT: B   59 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8613 (tppt)
REVERT: E   58 THR cc_start: 0.9540 (p) cc_final: 0.9284 (p)
REVERT: E  129 ARG cc_start: 0.8869 (ttm170) cc_final: 0.8645 (tpt90)
REVERT: F   25 ASN cc_start: 0.8641 (m110) cc_final: 0.8061 (m110)
REVERT: F   35 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8151 (mtp85)
REVERT: G   61 GLU cc_start: 0.9071 (tp30) cc_final: 0.8768 (tp30)
REVERT: H  105 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7939 (tt0)
REVERT: M   11 GLU cc_start: 0.8153 (mp0) cc_final: 0.7786 (pm20)
REVERT: M   92 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8410 (ttmm)
REVERT: P   30 MET cc_start: 0.8245 (mmm) cc_final: 0.8003 (mmm)
REVERT: P   49 VAL cc_start: 0.8194 (m) cc_final: 0.7979 (m)
  outliers start: 33
  outliers final: 22
  residues processed: 284
  average time/residue: 0.1562
  time to fit residues: 60.4576
Evaluate side-chains
  289 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 265
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain N residue   16 THR
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   63 THR
Chi-restraints excluded: chain P residue   36 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 139 optimal weight:    0.0020
   chunk 69 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 140 optimal weight:    0.0970
   overall best weight:    0.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  47 GLN
D  82 HIS
E  76 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  84 ASN
H 109 HIS
** M  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  77 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.098571 restraints weight = 22283.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.77
r_work: 0.2988 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.066  16300  Z= 0.129
  Angle     :  0.601   7.900  23252  Z= 0.343
  Chirality :  0.044   0.305   2644
  Planarity :  0.004   0.044   1942
  Dihedral  : 28.907 171.643   4475
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.24 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.25), residues: 1171
  helix:  0.94 (0.22), residues: 647
  sheet: -0.75 (0.67), residues: 68
  loop : -1.18 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  53 
 TYR   0.015   0.001   TYR C  57 
 PHE   0.032   0.002   PHE P  50 
 TRP   0.006   0.001   TRP N  17 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.13 (16286)
  covalent geometry    : angle       0.59990 /  0.34 (23240)
  hydrogen bonds       : bond        0.04220 /  2.84 (  725)
  hydrogen bonds       : angle       3.01340 /  2.11 ( 1833)
  metal coordination   : bond        0.01817 /  1.43 (   14)
  metal coordination   : angle       1.87222 /  1.19 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 270
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8100 (mmm-85)
REVERT: A   93 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8783 (mm-40)
REVERT: A  115 LYS cc_start: 0.9133 (mttm) cc_final: 0.8863 (mmtm)
REVERT: B   59 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8780 (tttp)
REVERT: E   58 THR cc_start: 0.9541 (p) cc_final: 0.9281 (p)
REVERT: E  129 ARG cc_start: 0.8888 (ttm170) cc_final: 0.8662 (tpt90)
REVERT: F   25 ASN cc_start: 0.8532 (m110) cc_final: 0.7939 (m110)
REVERT: F   35 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8155 (mtp85)
REVERT: G   61 GLU cc_start: 0.9058 (tp30) cc_final: 0.8752 (tp30)
REVERT: H  105 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7962 (tt0)
REVERT: M   11 GLU cc_start: 0.8181 (mp0) cc_final: 0.7830 (pm20)
REVERT: M   92 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8390 (ttmm)
REVERT: N   26 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.8070 (ttt-90)
  outliers start: 27
  outliers final: 19
  residues processed: 282
  average time/residue: 0.1732
  time to fit residues: 65.5824
Evaluate side-chains
  283 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 262
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain N residue   16 THR
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain P residue   73 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 109 optimal weight:    9.9990
   chunk 11 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 122 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 123 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
D  47 GLN
D  63 ASN
D  82 HIS
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  84 ASN
H 109 HIS
M  76 GLN
** N  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  77 ASN
P  79 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.136179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.095738 restraints weight = 21992.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.76
r_work: 0.2938 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  16300  Z= 0.168
  Angle     :  0.643  10.328  23252  Z= 0.358
  Chirality :  0.047   0.324   2644
  Planarity :  0.004   0.057   1942
  Dihedral  : 29.087 173.484   4475
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.05 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.25), residues: 1171
  helix:  0.92 (0.21), residues: 653
  sheet: -0.40 (0.76), residues: 58
  loop : -1.15 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 129 
 TYR   0.016   0.002   TYR H  42 
 PHE   0.021   0.002   PHE P  50 
 TRP   0.005   0.001   TRP P  93 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.17 (16286)
  covalent geometry    : angle       0.64223 /  0.36 (23240)
  hydrogen bonds       : bond        0.04540 /  3.04 (  725)
  hydrogen bonds       : angle       3.10101 /  2.17 ( 1833)
  metal coordination   : bond        0.01718 /  1.34 (   14)
  metal coordination   : angle       1.86556 /  1.23 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 273
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8140 (mmm-85)
REVERT: A   73 GLU cc_start: 0.8886 (tt0) cc_final: 0.8408 (tt0)
REVERT: A   93 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8819 (mm-40)
REVERT: A  115 LYS cc_start: 0.9114 (mttm) cc_final: 0.8843 (mmtm)
REVERT: B   59 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8787 (tttp)
REVERT: C  110 ASN cc_start: 0.8134 (m-40) cc_final: 0.7802 (p0)
REVERT: E   58 THR cc_start: 0.9558 (p) cc_final: 0.9300 (p)
REVERT: E  129 ARG cc_start: 0.8909 (ttm170) cc_final: 0.8663 (tpt90)
REVERT: F   35 ARG cc_start: 0.8878 (mtp85) cc_final: 0.8138 (mtp85)
REVERT: F   44 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8730 (mtpt)
REVERT: G   61 GLU cc_start: 0.9082 (tp30) cc_final: 0.8810 (tp30)
REVERT: H  105 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8013 (tp30)
REVERT: H  113 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7903 (mt-10)
REVERT: M   11 GLU cc_start: 0.8156 (mp0) cc_final: 0.7878 (pm20)
REVERT: M   92 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8324 (ttmm)
REVERT: N  101 ARG cc_start: 0.8849 (mmt-90) cc_final: 0.8589 (mmt-90)
  outliers start: 31
  outliers final: 22
  residues processed: 288
  average time/residue: 0.1833
  time to fit residues: 70.5430
Evaluate side-chains
  288 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 264
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain N residue   16 THR
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain P residue   36 THR
Chi-restraints excluded: chain P residue   73 ILE
Chi-restraints excluded: chain P residue   79 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 125 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 106 optimal weight:   20.0000
   chunk 25 optimal weight:    0.0270
   chunk 112 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.6038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  47 GLN
D  63 ASN
D  82 HIS
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  84 ASN
H 109 HIS
** P  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  77 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.137071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.096223 restraints weight = 22072.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.81
r_work: 0.2961 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2820
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2820
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.4294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  16300  Z= 0.130
  Angle     :  0.618   8.195  23252  Z= 0.348
  Chirality :  0.045   0.328   2644
  Planarity :  0.004   0.040   1942
  Dihedral  : 29.000 175.129   4475
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.93 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.25), residues: 1171
  helix:  1.05 (0.22), residues: 650
  sheet: -0.30 (0.76), residues: 58
  loop : -1.14 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  53 
 TYR   0.018   0.002   TYR H  42 
 PHE   0.023   0.001   PHE P  50 
 TRP   0.006   0.001   TRP P 141 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.13 (16286)
  covalent geometry    : angle       0.61689 /  0.35 (23240)
  hydrogen bonds       : bond        0.04258 /  2.87 (  725)
  hydrogen bonds       : angle       3.07554 /  2.16 ( 1833)
  metal coordination   : bond        0.01817 /  1.43 (   14)
  metal coordination   : angle       2.02143 /  1.28 (   12)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 271
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8795 (mm-40)
REVERT: A  115 LYS cc_start: 0.9118 (mttm) cc_final: 0.8844 (mmtm)
REVERT: B   59 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8750 (tttp)
REVERT: C  110 ASN cc_start: 0.8098 (m-40) cc_final: 0.7752 (p0)
REVERT: E   58 THR cc_start: 0.9536 (p) cc_final: 0.9273 (p)
REVERT: E  129 ARG cc_start: 0.8952 (ttm170) cc_final: 0.8627 (tpt90)
REVERT: F   35 ARG cc_start: 0.8918 (mtp85) cc_final: 0.8162 (mtp85)
REVERT: G   61 GLU cc_start: 0.9090 (tp30) cc_final: 0.8816 (tp30)
REVERT: H  105 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7855 (tp30)
REVERT: H  113 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7881 (mt-10)
REVERT: M   11 GLU cc_start: 0.8197 (mp0) cc_final: 0.7902 (pm20)
REVERT: M   92 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8428 (ttmm)
REVERT: N  101 ARG cc_start: 0.8850 (mmt-90) cc_final: 0.8446 (mmt-90)
  outliers start: 21
  outliers final: 18
  residues processed: 280
  average time/residue: 0.1875
  time to fit residues: 70.3870
Evaluate side-chains
  294 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 274
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  105 GLU
Chi-restraints excluded: chain M residue   32 ILE
Chi-restraints excluded: chain N residue   16 THR
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain P residue   36 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 129 optimal weight:    0.5980
   chunk 103 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0030
   overall best weight:    0.6392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
D  82 HIS
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  84 ASN
H 109 HIS
P  77 ASN
P  79 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.097100 restraints weight = 21944.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.79
r_work: 0.2976 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  16300  Z= 0.129
  Angle     :  0.600   7.894  23252  Z= 0.341
  Chirality :  0.044   0.326   2644
  Planarity :  0.004   0.055   1942
  Dihedral  : 28.898 177.872   4475
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.12 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.25), residues: 1171
  helix:  1.15 (0.22), residues: 649
  sheet: -0.22 (0.77), residues: 58
  loop : -1.10 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  53 
 TYR   0.019   0.001   TYR P  74 
 PHE   0.037   0.001   PHE P  50 
 TRP   0.010   0.001   TRP P 141 
 HIS   0.008   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.13 (16286)
  covalent geometry    : angle       0.59798 /  0.34 (23240)
  hydrogen bonds       : bond        0.04176 /  2.82 (  725)
  hydrogen bonds       : angle       3.02868 /  2.12 ( 1833)
  metal coordination   : bond        0.01910 /  1.51 (   14)
  metal coordination   : angle       2.05809 /  1.29 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4984.39 seconds
wall clock time: 85 minutes 23.34 seconds (5123.34 seconds total)