Starting phenix.real_space_refine
on Sat Jul  4 19:40:07 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xct_33127/07_2026/7xct_33127.map"
  }
  resolution = 2.72
  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=   0.107
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 5945 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: 5
    Type Number    sf(0)   Gaussians
     P     290      5.49       5
     S      40      5.16       5
     C   10853      2.51       5
     N    3399      2.21       5
     O    4051      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 18633
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "L"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 707
          Classifications: {'peptide': 88}
          Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 718
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "K"
      Number of atoms: 2656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2656
          Classifications: {'peptide': 326}
          Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 307}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    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: "M"
      Number of atoms: 2671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2671
          Classifications: {'peptide': 328}
          Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308}
    Chain: "N"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
    Chain: "M"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N   LEU L  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU L  73 " occ=0.45
    residue:
      pdb=" N   ARG L  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG L  74 " occ=0.45
    residue:
      pdb=" N   GLY L  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY L  75 " occ=0.25
    residue:
      pdb=" N   GLY L  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY L  76 " occ=0.25
    residue:
      pdb=" N   LEU N  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU N  73 " occ=0.45
    residue:
      pdb=" N   ARG N  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG N  74 " occ=0.45
    residue:
      pdb=" N   GLY N  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY N  75 " occ=0.25
    residue:
      pdb=" N   GLY N  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY N  76 " occ=0.25
  Time building chain proxies: 4.39, per 1000 atoms: 0.24
  Number of scatterers: 18633
  At special positions: 0
  Unit cell: (151.2, 123.12, 150.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P     290     15.00
     O    4051      8.00
     N    3399      7.00
     C   10853      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: 1.66
  Conformation dependent library (CDL) restraints added in 535.4 milliseconds
  

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2966

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 14 sheets defined
      51.5% alpha, 6.9% beta
      125 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 2.58
  Creating SS restraints...
    Processing helix  chain 'L' and resid 22 through 34
      removed outlier: 4.357A  pdb=" N   GLN L  31 " --> pdb=" O   LYS L  27 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP L  32 " --> pdb=" O   ALA L  28 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 56 through 60
      removed outlier: 3.803A  pdb=" N   ASN L  60 " --> pdb=" O   SER L  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 35
    Processing helix  chain 'F' and resid 36 through 41
      removed outlier: 3.726A  pdb=" N   ARG F  40 " --> pdb=" O   ARG F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 54
      removed outlier: 3.588A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.517A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.553A  pdb=" N   GLU H  71 " --> pdb=" O   ASN H  67 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
    Processing helix  chain 'K' and resid 36 through 45
      removed outlier: 3.689A  pdb=" N   ARG K  42 " --> pdb=" O   ILE K  38 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TRP K  43 " --> pdb=" O   GLU K  39 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL K  44 " --> pdb=" O   THR K  40 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 50 through 55
    Processing helix  chain 'K' and resid 68 through 73
    Processing helix  chain 'K' and resid 75 through 80
    Processing helix  chain 'K' and resid 82 through 87
    Processing helix  chain 'K' and resid 88 through 90
      No H-bonds generated for 'chain 'K' and resid 88 through 90'
    Processing helix  chain 'K' and resid 105 through 119
      removed outlier: 3.599A  pdb=" N   HIS K 109 " --> pdb=" O   GLY K 105 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN K 116 " --> pdb=" O   GLN K 112 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 121 through 127
    Processing helix  chain 'K' and resid 140 through 152
    Processing helix  chain 'K' and resid 167 through 175
      removed outlier: 3.577A  pdb=" N   LEU K 171 " --> pdb=" O   GLY K 167 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 188 through 209
      removed outlier: 3.540A  pdb=" N   GLU K 196 " --> pdb=" O   ALA K 192 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   THR K 197 " --> pdb=" O   LYS K 193 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG K 203 " --> pdb=" O   ASP K 199 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TYR K 209 " --> pdb=" O   TRP K 205 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 225 through 234
      removed outlier: 4.366A  pdb=" N   GLU K 230 " --> pdb=" O   GLU K 226 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG K 231 " --> pdb=" O   GLU K 227 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA K 233 " --> pdb=" O   ARG K 229 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 255
      removed outlier: 3.738A  pdb=" N   GLU K 255 " --> pdb=" O   HIS K 251 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 256 through 260
      removed outlier: 3.817A  pdb=" N   ASN K 259 " --> pdb=" O   ARG K 256 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 286 through 289
    Processing helix  chain 'K' and resid 320 through 325
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 76 through 79
      removed outlier: 3.614A  pdb=" N   NLE E  79 " --> pdb=" O   GLN E  76 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 76 through 79'
    Processing helix  chain 'E' and resid 85 through 113
      removed outlier: 3.576A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASP E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.626A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.525A  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: 3.605A  pdb=" N   ASP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.655A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.551A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   HIS D  82 " --> pdb=" O   SER D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
      removed outlier: 3.612A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.746A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.601A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 36 through 45
      removed outlier: 3.690A  pdb=" N   ARG M  42 " --> pdb=" O   ILE M  38 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TRP M  43 " --> pdb=" O   GLU M  39 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL M  44 " --> pdb=" O   THR M  40 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 50 through 55
    Processing helix  chain 'M' and resid 68 through 73
    Processing helix  chain 'M' and resid 75 through 80
    Processing helix  chain 'M' and resid 82 through 87
    Processing helix  chain 'M' and resid 88 through 90
      No H-bonds generated for 'chain 'M' and resid 88 through 90'
    Processing helix  chain 'M' and resid 105 through 119
      removed outlier: 3.599A  pdb=" N   HIS M 109 " --> pdb=" O   GLY M 105 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN M 116 " --> pdb=" O   GLN M 112 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 121 through 127
    Processing helix  chain 'M' and resid 140 through 152
    Processing helix  chain 'M' and resid 167 through 175
      removed outlier: 3.577A  pdb=" N   LEU M 171 " --> pdb=" O   GLY M 167 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 188 through 209
      removed outlier: 3.540A  pdb=" N   GLU M 196 " --> pdb=" O   ALA M 192 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   THR M 197 " --> pdb=" O   LYS M 193 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG M 203 " --> pdb=" O   ASP M 199 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TYR M 209 " --> pdb=" O   TRP M 205 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 225 through 234
      removed outlier: 4.366A  pdb=" N   GLU M 230 " --> pdb=" O   GLU M 226 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ARG M 231 " --> pdb=" O   GLU M 227 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA M 233 " --> pdb=" O   ARG M 229 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 246 through 255
      removed outlier: 3.737A  pdb=" N   GLU M 255 " --> pdb=" O   HIS M 251 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 256 through 260
      removed outlier: 3.817A  pdb=" N   ASN M 259 " --> pdb=" O   ARG M 256 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 286 through 289
    Processing helix  chain 'M' and resid 320 through 325
    Processing helix  chain 'N' and resid 22 through 34
      removed outlier: 4.357A  pdb=" N   GLN N  31 " --> pdb=" O   LYS N  27 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP N  32 " --> pdb=" O   ALA N  28 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 56 through 60
      removed outlier: 3.802A  pdb=" N   ASN N  60 " --> pdb=" O   SER N  57 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 12 through 15
      removed outlier: 3.566A  pdb=" N   VAL L   5 " --> pdb=" O   ILE L  13 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE L   4 " --> pdb=" O   LEU L  67 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   LEU L  69 " --> pdb=" O   PHE L   4 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   LYS L   6 " --> pdb=" O   LEU L  69 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   LEU L  71 " --> pdb=" O   LYS L   6 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   HIS L  68 " --> pdb=" O   ILE L  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 46
      removed outlier: 7.167A  pdb=" N   ARG F  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98
      removed outlier: 6.417A  pdb=" N   THR F  96 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.147A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'K' and resid 7 through 8
      removed outlier: 3.558A  pdb=" N   LEU K   7 " --> pdb=" O   TYR K  20 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 215 through 220
      removed outlier: 6.418A  pdb=" N   HIS K 182 " --> pdb=" O   THR K 217 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   GLU K 219 " --> pdb=" O   HIS K 182 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLY K 184 " --> pdb=" O   GLU K 219 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   PHE K 159 " --> pdb=" O   TYR K 183 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   VAL K 185 " --> pdb=" O   PHE K 159 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP K 161 " --> pdb=" O   VAL K 185 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE K 238 " --> pdb=" O   VAL K 267 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.199A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AB3, first strand: chain 'M' and resid 7 through 8
      removed outlier: 3.559A  pdb=" N   LEU M   7 " --> pdb=" O   TYR M  20 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 215 through 220
      removed outlier: 6.417A  pdb=" N   HIS M 182 " --> pdb=" O   THR M 217 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   GLU M 219 " --> pdb=" O   HIS M 182 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLY M 184 " --> pdb=" O   GLU M 219 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   PHE M 159 " --> pdb=" O   TYR M 183 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   VAL M 185 " --> pdb=" O   PHE M 159 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ASP M 161 " --> pdb=" O   VAL M 185 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE M 238 " --> pdb=" O   VAL M 267 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 12 through 15
      removed outlier: 3.566A  pdb=" N   VAL N   5 " --> pdb=" O   ILE N  13 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE N   4 " --> pdb=" O   LEU N  67 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LEU N  69 " --> pdb=" O   PHE N   4 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   LYS N   6 " --> pdb=" O   LEU N  69 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   LEU N  71 " --> pdb=" O   LYS N   6 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   HIS N  68 " --> pdb=" O   ILE N  44 " (cutoff:3.500A)

    526 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      305 hydrogen bonds
      590 hydrogen bond angles
      0 basepair planarities
      125 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 3.63

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2539
        1.31 -     1.44: 6617
        1.44 -     1.56: 9780
        1.56 -     1.69: 582
        1.69 -     1.81: 74
  Bond restraints: 19592
  Sorted by residual:
  bond pdb=" C1'  DC J  65 "
       pdb=" N1   DC J  65 "
    ideal  model  delta    sigma   weight residual
    1.468  1.595 -0.127 1.40e-02 5.10e+03 8.22e+01
  bond pdb=" C3'  DG J  94 "
       pdb=" O3'  DG J  94 "
    ideal  model  delta    sigma   weight residual
    1.435  1.498 -0.063 1.30e-02 5.92e+03 2.38e+01
  bond pdb=" N1   DC I  70 "
       pdb=" C6   DC I  70 "
    ideal  model  delta    sigma   weight residual
    1.367  1.338  0.029 6.00e-03 2.78e+04 2.31e+01
  bond pdb=" C3'  DG J  69 "
       pdb=" O3'  DG J  69 "
    ideal  model  delta    sigma   weight residual
    1.435  1.374  0.061 1.30e-02 5.92e+03 2.21e+01
  bond pdb=" C3'  DA I  69 "
       pdb=" O3'  DA I  69 "
    ideal  model  delta    sigma   weight residual
    1.435  1.376  0.059 1.30e-02 5.92e+03 2.05e+01
  ... (remaining 19587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.96: 27440
        3.96 -     7.91: 237
        7.91 -    11.87: 45
       11.87 -    15.82: 3
       15.82 -    19.78: 4
  Bond angle restraints: 27729
  Sorted by residual:
  angle pdb=" C   GLU M  47 "
        pdb=" N   ILE M  48 "
        pdb=" CA  ILE M  48 "
      ideal   model   delta    sigma   weight residual
     121.70  141.48  -19.78 1.80e+00 3.09e-01 1.21e+02
  angle pdb=" C   GLU K  47 "
        pdb=" N   ILE K  48 "
        pdb=" CA  ILE K  48 "
      ideal   model   delta    sigma   weight residual
     121.70  141.47  -19.77 1.80e+00 3.09e-01 1.21e+02
  angle pdb=" C   ARG F  67 "
        pdb=" N   ASP F  68 "
        pdb=" CA  ASP F  68 "
      ideal   model   delta    sigma   weight residual
     121.54  135.56  -14.02 1.91e+00 2.74e-01 5.39e+01
  angle pdb=" C   TYR F  88 "
        pdb=" CA  TYR F  88 "
        pdb=" CB  TYR F  88 "
      ideal   model   delta    sigma   weight residual
     109.83  103.87    5.96 9.90e-01 1.02e+00 3.62e+01
  angle pdb=" O4'  DC J  65 "
        pdb=" C1'  DC J  65 "
        pdb=" N1   DC J  65 "
      ideal   model   delta    sigma   weight residual
     108.00  111.85   -3.85 7.00e-01 2.04e+00 3.03e+01
  ... (remaining 27724 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 9703
       35.58 -    71.16: 1320
       71.16 -   106.74: 13
      106.74 -   142.32: 1
      142.32 -   177.90: 2
  Dihedral angle restraints: 11039
    sinusoidal: 6448
      harmonic: 4591
  Sorted by residual:
  dihedral pdb=" CA  TRP K  22 "
           pdb=" C   TRP K  22 "
           pdb=" N   PRO K  23 "
           pdb=" CA  PRO K  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -106.89  -73.11     0      5.00e+00 4.00e-02 2.14e+02
  dihedral pdb=" CA  TRP M  22 "
           pdb=" C   TRP M  22 "
           pdb=" N   PRO M  23 "
           pdb=" CA  PRO M  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -106.90  -73.10     0      5.00e+00 4.00e-02 2.14e+02
  dihedral pdb=" CA  GLN F  27 "
           pdb=" C   GLN F  27 "
           pdb=" N   GLY F  28 "
           pdb=" CA  GLY F  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  115.38   64.62     0      5.00e+00 4.00e-02 1.67e+02
  ... (remaining 11036 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 2243
       0.071 -    0.142: 757
       0.142 -    0.213: 100
       0.213 -    0.284: 13
       0.284 -    0.354: 4
  Chirality restraints: 3117
  Sorted by residual:
  chirality pdb=" CB  VAL F  43 "
            pdb=" CA  VAL F  43 "
            pdb=" CG1 VAL F  43 "
            pdb=" CG2 VAL F  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.35 2.00e-01 2.50e+01 3.14e+00
  chirality pdb=" CB  ILE M  48 "
            pdb=" CA  ILE M  48 "
            pdb=" CG1 ILE M  48 "
            pdb=" CG2 ILE M  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.97   -0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  ILE K  48 "
            pdb=" CA  ILE K  48 "
            pdb=" CG1 ILE K  48 "
            pdb=" CG2 ILE K  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.97   -0.32 2.00e-01 2.50e+01 2.63e+00
  ... (remaining 3114 not shown)

  Planarity restraints: 2519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP K  22 "   -0.054 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO K  23 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO K  23 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO K  23 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  25 "   -0.025 2.00e-02 2.50e+03   2.45e-02 1.05e+01
        pdb=" CG  PHE G  25 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  25 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  25 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  25 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  25 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  25 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP M  22 "    0.054 5.00e-02 4.00e+02   8.11e-02 1.05e+01
        pdb=" N   PRO M  23 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO M  23 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO M  23 "    0.044 5.00e-02 4.00e+02
  ... (remaining 2516 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2964
        2.76 -     3.29: 15464
        3.29 -     3.83: 33115
        3.83 -     4.36: 42587
        4.36 -     4.90: 63026
  Nonbonded interactions: 157156
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  82 "
            pdb=" O   MET F  84 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OP1  DG J 125 "
            pdb=" O   LEU N  73 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OE2 GLU K 186 "
            pdb=" O2' SAM K 500 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE2 GLU M 186 "
            pdb=" O2' SAM M 500 "
     model   vdw
     2.303 3.040
  ... (remaining 157151 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 135)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 33 through 124)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = (chain 'M' and (resid 5 through 330 or resid 500))
}
ncs_group {
  reference = chain 'L'
  selection = chain 'N'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.960
  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:             0.020
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     19.590
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
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      :  0.012   0.127  19592  Z= 0.876
  Angle     :  1.177  19.779  27729  Z= 0.793
  Chirality :  0.068   0.354   3117
  Planarity :  0.008   0.081   2519
  Dihedral  : 22.726 177.902   8073
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.31 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  3.83 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    Twisted General : 0.33 %

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: -5.11 (0.15), residues: 1545
  helix: -4.25 (0.08), residues: 783
  sheet: -1.05 (0.48), residues: 142
  loop : -2.50 (0.20), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG B  78 
 TYR   0.046   0.003   TYR M 312 
 PHE   0.056   0.004   PHE G  25 
 TRP   0.036   0.005   TRP K  22 
 HIS   0.018   0.003   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01249 /  0.88 (19592)
  covalent geometry    : angle       1.17699 /  0.79 (27729)
  hydrogen bonds       : bond        0.30837 / 20.57 (  831)
  hydrogen bonds       : angle       9.45175 /  6.53 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 266
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   77 ASP cc_start: 0.8156 (m-30) cc_final: 0.7937 (m-30)
REVERT: A  122 LYS cc_start: 0.8973 (pttt) cc_final: 0.8742 (pttp)
REVERT: D   59 MET cc_start: 0.8960 (tpp) cc_final: 0.8684 (tpp)
REVERT: D   88 THR cc_start: 0.9058 (t) cc_final: 0.8647 (m)
REVERT: M   71 MET cc_start: 0.4126 (mmt) cc_final: 0.3497 (tpp)
  outliers start: 8
  outliers final: 4
  residues processed: 274
  average time/residue: 0.9316
  time to fit residues: 275.0005
Evaluate side-chains
  181 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 177
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:   30.0000
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  60 ASN
F  18 HIS
F  64 ASN
G  24 GLN
G  73 ASN
G  82 HIS
H  63 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  31 HIS
K  79 ASN
K  99 ASN
K 112 GLN
K 113 GLN
E  68 GLN
E  76 GLN
A 113 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
C  24 GLN
C  82 HIS
B  25 ASN
M  31 HIS
M  79 ASN
M 117 HIS
** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 331 ASN
N  60 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.173820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127870 restraints weight = 23327.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.27
r_work: 0.3297 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  19592  Z= 0.175
  Angle     :  0.803  15.181  27729  Z= 0.445
  Chirality :  0.054   0.295   3117
  Planarity :  0.006   0.075   2519
  Dihedral  : 28.023 166.568   4916
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.85 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 10.31 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    Twisted General : 0.40 %

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: -2.40 (0.20), residues: 1545
  helix: -1.44 (0.16), residues: 799
  sheet: -0.72 (0.49), residues: 140
  loop : -1.83 (0.23), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  72 
 TYR   0.016   0.001   TYR K 312 
 PHE   0.022   0.002   PHE K 223 
 TRP   0.019   0.002   TRP M  22 
 HIS   0.006   0.001   HIS G  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.17 (19592)
  covalent geometry    : angle       0.80300 /  0.45 (27729)
  hydrogen bonds       : bond        0.07726 /  5.12 (  831)
  hydrogen bonds       : angle       4.13281 /  2.81 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 198
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7743 (tptt)
REVERT: G   95 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8566 (ttmm)
REVERT: H   47 GLN cc_start: 0.8724 (mt0) cc_final: 0.8492 (mt0)
REVERT: K   71 MET cc_start: 0.5162 (OUTLIER) cc_final: 0.4664 (mpp)
REVERT: K  177 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7598 (p)
REVERT: K  212 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7306 (mtpt)
REVERT: E   73 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8429 (tt0)
REVERT: A  120 MET cc_start: 0.8899 (mtm) cc_final: 0.8451 (mtm)
REVERT: A  122 LYS cc_start: 0.9068 (pttt) cc_final: 0.8860 (pttp)
REVERT: M   71 MET cc_start: 0.4911 (mmt) cc_final: 0.4195 (tpp)
  outliers start: 44
  outliers final: 12
  residues processed: 222
  average time/residue: 0.8416
  time to fit residues: 202.9004
Evaluate side-chains
  195 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain M residue  297 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 75 optimal weight:    4.9990
   chunk 112 optimal weight:   30.0000
   chunk 131 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0970
   chunk 87 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 170 optimal weight:    4.9990
   chunk 151 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 159 optimal weight:    8.9990
   overall best weight:    3.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
G  73 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 GLN
E  39 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.169745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.120546 restraints weight = 22829.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.39
r_work: 0.3197 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  19592  Z= 0.237
  Angle     :  0.782  14.956  27729  Z= 0.429
  Chirality :  0.054   0.326   3117
  Planarity :  0.006   0.074   2519
  Dihedral  : 28.357 160.860   4914
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.50 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 12.22 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -1.36 (0.21), residues: 1545
  helix: -0.35 (0.18), residues: 803
  sheet: -0.52 (0.48), residues: 140
  loop : -1.64 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  71 
 TYR   0.022   0.002   TYR K 312 
 PHE   0.026   0.002   PHE K 223 
 TRP   0.014   0.002   TRP M  22 
 HIS   0.009   0.001   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00517 /  0.24 (19592)
  covalent geometry    : angle       0.78200 /  0.43 (27729)
  hydrogen bonds       : bond        0.07191 /  4.79 (  831)
  hydrogen bonds       : angle       3.79022 /  2.57 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 183
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.6560 (mttt)
REVERT: G   91 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8632 (tt0)
REVERT: K   71 MET cc_start: 0.5147 (OUTLIER) cc_final: 0.4592 (mpp)
REVERT: K  104 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8295 (t)
REVERT: E   53 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8234 (ttt180)
REVERT: E   73 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8406 (tt0)
REVERT: A   59 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8498 (pm20)
REVERT: D   59 MET cc_start: 0.9208 (tpp) cc_final: 0.8916 (tpt)
REVERT: D   96 THR cc_start: 0.8890 (t) cc_final: 0.8671 (p)
REVERT: C   36 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8139 (ptpt)
REVERT: C   91 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8221 (tt0)
REVERT: M   22 TRP cc_start: 0.3386 (OUTLIER) cc_final: 0.2969 (t-100)
REVERT: M   71 MET cc_start: 0.5056 (mmt) cc_final: 0.4387 (tpp)
  outliers start: 55
  outliers final: 27
  residues processed: 215
  average time/residue: 0.7658
  time to fit residues: 180.0086
Evaluate side-chains
  214 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 178
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain K residue   22 TRP
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  106 LEU
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  200 ARG
Chi-restraints excluded: chain M residue  297 SER
Chi-restraints excluded: chain M residue  329 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 165 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 111 optimal weight:   40.0000
   chunk 143 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
K 112 GLN
A  68 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 113 GLN
** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 252 GLN
** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.171745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.122585 restraints weight = 22806.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.33
r_work: 0.3239 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  19592  Z= 0.158
  Angle     :  0.726  14.639  27729  Z= 0.399
  Chirality :  0.050   0.311   3117
  Planarity :  0.005   0.079   2519
  Dihedral  : 28.341 164.292   4914
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.31 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 13.48 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -0.84 (0.22), residues: 1545
  helix:  0.17 (0.19), residues: 800
  sheet: -0.36 (0.48), residues: 140
  loop : -1.51 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  86 
 TYR   0.015   0.001   TYR M 209 
 PHE   0.018   0.001   PHE K 223 
 TRP   0.012   0.002   TRP M  22 
 HIS   0.006   0.001   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.16 (19592)
  covalent geometry    : angle       0.72634 /  0.40 (27729)
  hydrogen bonds       : bond        0.06111 /  4.02 (  831)
  hydrogen bonds       : angle       3.59234 /  2.44 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 183
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   23 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7467 (tpp-160)
REVERT: G   13 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.6568 (mttt)
REVERT: H   47 GLN cc_start: 0.8750 (mt0) cc_final: 0.8469 (mt0)
REVERT: K   55 MET cc_start: 0.3205 (mtm) cc_final: 0.1615 (mmt)
REVERT: K   71 MET cc_start: 0.5266 (OUTLIER) cc_final: 0.4753 (mpp)
REVERT: K  104 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8287 (t)
REVERT: K  129 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8097 (tt0)
REVERT: K  276 ASN cc_start: 0.7494 (p0) cc_final: 0.7264 (p0)
REVERT: E   73 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8346 (tt0)
REVERT: A   59 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8316 (pm20)
REVERT: D   59 MET cc_start: 0.9155 (tpp) cc_final: 0.8851 (tpt)
REVERT: D   96 THR cc_start: 0.8870 (t) cc_final: 0.8618 (p)
REVERT: C   36 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8126 (ptpt)
REVERT: C   59 THR cc_start: 0.8991 (t) cc_final: 0.8781 (p)
REVERT: C   91 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8145 (tt0)
REVERT: M   22 TRP cc_start: 0.3433 (OUTLIER) cc_final: 0.3070 (t-100)
REVERT: M   71 MET cc_start: 0.5051 (mmt) cc_final: 0.4414 (tpp)
  outliers start: 46
  outliers final: 24
  residues processed: 210
  average time/residue: 0.7470
  time to fit residues: 172.1576
Evaluate side-chains
  207 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  129 GLU
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue  106 LEU
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  200 ARG
Chi-restraints excluded: chain M residue  297 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 145 optimal weight:    9.9990
   chunk 135 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 121 optimal weight:    9.9990
   chunk 133 optimal weight:    9.9990
   chunk 153 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 123 optimal weight:   30.0000
   chunk 168 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 GLN
E  68 GLN
E  85 GLN
A  68 GLN
A  76 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
M 113 GLN
** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.167248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118146 restraints weight = 22625.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.38
r_work: 0.3094 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2953
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.089  19592  Z= 0.382
  Angle     :  0.889  14.845  27729  Z= 0.474
  Chirality :  0.061   0.351   3117
  Planarity :  0.007   0.084   2519
  Dihedral  : 28.520 157.373   4914
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.95 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 12.81 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    Twisted General : 0.33 %

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: -1.10 (0.21), residues: 1545
  helix: -0.09 (0.19), residues: 806
  sheet: -0.37 (0.47), residues: 140
  loop : -1.62 (0.24), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  40 
 TYR   0.021   0.003   TYR K 312 
 PHE   0.028   0.003   PHE K 223 
 TRP   0.015   0.003   TRP K 228 
 HIS   0.013   0.002   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00859 /  0.38 (19592)
  covalent geometry    : angle       0.88875 /  0.47 (27729)
  hydrogen bonds       : bond        0.08223 /  5.50 (  831)
  hydrogen bonds       : angle       3.81029 /  2.59 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 174
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.6626 (mttt)
REVERT: G   91 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8650 (tt0)
REVERT: G   92 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8372 (mt-10)
REVERT: H   37 TYR cc_start: 0.9348 (m-80) cc_final: 0.9133 (m-80)
REVERT: K   55 MET cc_start: 0.2101 (mtm) cc_final: 0.0800 (mmt)
REVERT: K   71 MET cc_start: 0.5347 (OUTLIER) cc_final: 0.4847 (mpp)
REVERT: K  104 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8357 (t)
REVERT: A   59 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8269 (pm20)
REVERT: A  129 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7511 (tpt-90)
REVERT: C   36 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8176 (ptpt)
REVERT: C   91 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8236 (tt0)
REVERT: M   22 TRP cc_start: 0.3665 (OUTLIER) cc_final: 0.3296 (t-100)
REVERT: M   71 MET cc_start: 0.4989 (mmt) cc_final: 0.4350 (tpp)
  outliers start: 66
  outliers final: 35
  residues processed: 217
  average time/residue: 0.7606
  time to fit residues: 180.9179
Evaluate side-chains
  210 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 166
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   96 THR
Chi-restraints excluded: chain K residue   22 TRP
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue  106 LEU
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  200 ARG
Chi-restraints excluded: chain M residue  226 GLU
Chi-restraints excluded: chain M residue  297 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 162 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 111 optimal weight:   40.0000
   chunk 129 optimal weight:   10.0000
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 112 GLN
K 324 ASN
E  68 GLN
E  85 GLN
A  68 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 113 GLN
** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 252 GLN
M 315 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.171364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123110 restraints weight = 22562.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.29
r_work: 0.3234 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (10 function evaluations)
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  19592  Z= 0.147
  Angle     :  0.726  14.528  27729  Z= 0.396
  Chirality :  0.050   0.248   3117
  Planarity :  0.005   0.086   2519
  Dihedral  : 28.501 164.989   4914
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.24 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 14.29 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -0.61 (0.22), residues: 1545
  helix:  0.35 (0.19), residues: 809
  sheet: -0.20 (0.48), residues: 140
  loop : -1.43 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.011   0.001   TYR D  37 
 PHE   0.016   0.001   PHE M 223 
 TRP   0.013   0.002   TRP M  22 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 (19592)
  covalent geometry    : angle       0.72607 /  0.40 (27729)
  hydrogen bonds       : bond        0.05929 /  3.87 (  831)
  hydrogen bonds       : angle       3.46951 /  2.36 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 183
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   92 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8163 (mt-10)
REVERT: K   55 MET cc_start: 0.2497 (mtm) cc_final: 0.1085 (mmt)
REVERT: K  104 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8310 (t)
REVERT: K  170 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8885 (t)
REVERT: K  276 ASN cc_start: 0.7536 (p0) cc_final: 0.7328 (p0)
REVERT: D   96 THR cc_start: 0.8863 (t) cc_final: 0.8611 (p)
REVERT: C   36 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8235 (ptpt)
REVERT: C   91 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8089 (tt0)
REVERT: M   22 TRP cc_start: 0.3923 (OUTLIER) cc_final: 0.3665 (t-100)
REVERT: M   71 MET cc_start: 0.5116 (mmt) cc_final: 0.4477 (tpp)
  outliers start: 52
  outliers final: 27
  residues processed: 214
  average time/residue: 0.7587
  time to fit residues: 177.8337
Evaluate side-chains
  207 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue  106 LEU
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  297 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 137 optimal weight:   20.0000
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 112 optimal weight:   30.0000
   chunk 136 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 123 optimal weight:   30.0000
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   overall best weight:    2.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 112 GLN
A  68 GLN
D  84 ASN
M 113 GLN
** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.169361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.121661 restraints weight = 22801.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.24
r_work: 0.3209 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  19592  Z= 0.196
  Angle     :  0.725  14.294  27729  Z= 0.397
  Chirality :  0.051   0.268   3117
  Planarity :  0.005   0.087   2519
  Dihedral  : 28.402 160.479   4914
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.83 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 14.21 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -0.52 (0.22), residues: 1545
  helix:  0.42 (0.19), residues: 808
  sheet: -0.12 (0.48), residues: 140
  loop : -1.40 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  39 
 TYR   0.011   0.002   TYR M 209 
 PHE   0.019   0.002   PHE K 223 
 TRP   0.014   0.002   TRP M  22 
 HIS   0.008   0.001   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.20 (19592)
  covalent geometry    : angle       0.72471 /  0.40 (27729)
  hydrogen bonds       : bond        0.06177 /  4.08 (  831)
  hydrogen bonds       : angle       3.44561 /  2.35 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 180
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   91 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8546 (tt0)
REVERT: G   92 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8180 (mt-10)
REVERT: H   37 TYR cc_start: 0.9232 (m-80) cc_final: 0.8919 (m-80)
REVERT: K   55 MET cc_start: 0.2948 (mtm) cc_final: 0.1493 (mmt)
REVERT: K  104 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8350 (t)
REVERT: K  129 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8123 (tt0)
REVERT: K  276 ASN cc_start: 0.7569 (p0) cc_final: 0.7344 (p0)
REVERT: A   59 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8316 (pm20)
REVERT: A  120 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.7824 (mtt)
REVERT: A  129 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7459 (tpt-90)
REVERT: D   96 THR cc_start: 0.8893 (t) cc_final: 0.8650 (p)
REVERT: C   36 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8254 (ptpt)
REVERT: C   91 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8099 (tt0)
REVERT: M   22 TRP cc_start: 0.3822 (OUTLIER) cc_final: 0.3549 (t-100)
REVERT: M   71 MET cc_start: 0.5053 (mmt) cc_final: 0.4402 (tpp)
REVERT: M  180 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7349 (mmtm)
REVERT: M  248 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7678 (mm-30)
  outliers start: 53
  outliers final: 29
  residues processed: 216
  average time/residue: 0.8044
  time to fit residues: 190.3574
Evaluate side-chains
  219 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue   48 ILE
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  129 GLU
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue  106 LEU
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  180 LYS
Chi-restraints excluded: chain M residue  248 GLU
Chi-restraints excluded: chain M residue  297 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 115 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 4 optimal weight:   30.0000
   chunk 127 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 170 optimal weight:    6.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 112 GLN
A  68 GLN
M 113 GLN
M 252 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.170668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.121618 restraints weight = 22614.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.33
r_work: 0.3212 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  19592  Z= 0.156
  Angle     :  0.712  14.317  27729  Z= 0.390
  Chirality :  0.049   0.258   3117
  Planarity :  0.005   0.089   2519
  Dihedral  : 28.397 160.729   4914
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.95 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 14.51 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -0.42 (0.22), residues: 1545
  helix:  0.51 (0.19), residues: 808
  sheet: -0.07 (0.48), residues: 140
  loop : -1.37 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  39 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.018   0.001   PHE K 223 
 TRP   0.013   0.002   TRP M  22 
 HIS   0.007   0.001   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.16 (19592)
  covalent geometry    : angle       0.71206 /  0.39 (27729)
  hydrogen bonds       : bond        0.05944 /  3.91 (  831)
  hydrogen bonds       : angle       3.42295 /  2.33 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 182
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   92 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8280 (mt-10)
REVERT: K   55 MET cc_start: 0.2926 (mtm) cc_final: 0.1502 (mmt)
REVERT: K  104 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8352 (t)
REVERT: K  129 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (tt0)
REVERT: K  170 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8885 (t)
REVERT: K  276 ASN cc_start: 0.7575 (p0) cc_final: 0.7358 (p0)
REVERT: A   59 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8325 (pm20)
REVERT: A  120 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7805 (mtt)
REVERT: A  129 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7488 (tpt-90)
REVERT: D   96 THR cc_start: 0.8869 (t) cc_final: 0.8628 (p)
REVERT: C   36 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8244 (ptpt)
REVERT: C   59 THR cc_start: 0.9025 (t) cc_final: 0.8813 (p)
REVERT: C   91 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8148 (tt0)
REVERT: M   22 TRP cc_start: 0.3807 (OUTLIER) cc_final: 0.3525 (t-100)
REVERT: M  121 ASP cc_start: 0.7936 (t0) cc_final: 0.7709 (t70)
REVERT: M  180 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7322 (mmtm)
REVERT: M  248 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7690 (mm-30)
  outliers start: 51
  outliers final: 33
  residues processed: 214
  average time/residue: 0.7729
  time to fit residues: 181.4035
Evaluate side-chains
  224 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 180
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue   48 ILE
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  129 GLU
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue   61 ILE
Chi-restraints excluded: chain M residue  106 LEU
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  180 LYS
Chi-restraints excluded: chain M residue  226 GLU
Chi-restraints excluded: chain M residue  248 GLU
Chi-restraints excluded: chain M residue  297 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 174 optimal weight:    0.0770
   chunk 133 optimal weight:    9.9990
   chunk 125 optimal weight:   50.0000
   chunk 90 optimal weight:    0.9980
   chunk 155 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.9942

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M 113 GLN
M 252 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.171344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122498 restraints weight = 22569.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.32
r_work: 0.3226 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  19592  Z= 0.138
  Angle     :  0.694  14.470  27729  Z= 0.382
  Chirality :  0.049   0.282   3117
  Planarity :  0.005   0.089   2519
  Dihedral  : 28.378 161.643   4914
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.76 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.02 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -0.32 (0.22), residues: 1545
  helix:  0.62 (0.19), residues: 807
  sheet: -0.03 (0.48), residues: 140
  loop : -1.36 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.017   0.001   PHE K 223 
 TRP   0.013   0.002   TRP M  22 
 HIS   0.006   0.001   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.14 (19592)
  covalent geometry    : angle       0.69417 /  0.38 (27729)
  hydrogen bonds       : bond        0.05701 /  3.73 (  831)
  hydrogen bonds       : angle       3.38291 /  2.30 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 180
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   92 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8262 (mt-10)
REVERT: K   55 MET cc_start: 0.2679 (mtm) cc_final: 0.1741 (mmt)
REVERT: K  104 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8317 (t)
REVERT: K  129 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8118 (tt0)
REVERT: K  170 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8899 (t)
REVERT: A   59 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8309 (pm20)
REVERT: A  120 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7993 (mtt)
REVERT: A  129 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7481 (tpt-90)
REVERT: D   96 THR cc_start: 0.8886 (t) cc_final: 0.8600 (p)
REVERT: C   36 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8263 (ptpt)
REVERT: C   91 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8081 (tt0)
REVERT: M   22 TRP cc_start: 0.3679 (OUTLIER) cc_final: 0.3400 (t-100)
REVERT: M   71 MET cc_start: 0.4868 (mmt) cc_final: 0.4219 (tpp)
REVERT: M  121 ASP cc_start: 0.7949 (t0) cc_final: 0.7719 (t70)
REVERT: M  180 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7288 (mmtm)
REVERT: M  248 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7674 (mm-30)
  outliers start: 46
  outliers final: 30
  residues processed: 208
  average time/residue: 0.7346
  time to fit residues: 168.2710
Evaluate side-chains
  217 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 176
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain K residue   22 TRP
Chi-restraints excluded: chain K residue   48 ILE
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  129 GLU
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  177 THR
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue  106 LEU
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  180 LYS
Chi-restraints excluded: chain M residue  248 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 177 optimal weight:    0.4980
   chunk 173 optimal weight:   20.0000
   chunk 106 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 121 optimal weight:   10.9990
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 143 optimal weight:    8.9990
   chunk 175 optimal weight:   10.0000
   chunk 172 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  85 GLN
M 113 GLN
M 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.170615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.121394 restraints weight = 22682.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.35
r_work: 0.3214 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084  19592  Z= 0.176
  Angle     :  0.703  14.790  27729  Z= 0.386
  Chirality :  0.049   0.265   3117
  Planarity :  0.005   0.089   2519
  Dihedral  : 28.328 160.289   4914
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.89 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.54 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -0.28 (0.22), residues: 1545
  helix:  0.63 (0.19), residues: 807
  sheet:  0.03 (0.48), residues: 140
  loop : -1.31 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  39 
 TYR   0.010   0.001   TYR K  20 
 PHE   0.019   0.001   PHE K 223 
 TRP   0.013   0.002   TRP M  22 
 HIS   0.007   0.001   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.18 (19592)
  covalent geometry    : angle       0.70262 /  0.39 (27729)
  hydrogen bonds       : bond        0.05885 /  3.87 (  831)
  hydrogen bonds       : angle       3.35295 /  2.29 ( 2108)

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

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

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3090 Ramachandran restraints generated.
    1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 180
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   37 TYR cc_start: 0.9218 (m-80) cc_final: 0.8933 (m-80)
REVERT: K   55 MET cc_start: 0.2788 (mtm) cc_final: 0.1833 (mmt)
REVERT: K  104 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8415 (t)
REVERT: K  129 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8120 (tt0)
REVERT: A  120 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7977 (mtt)
REVERT: A  129 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7504 (tpt-90)
REVERT: D   96 THR cc_start: 0.8904 (t) cc_final: 0.8611 (p)
REVERT: C   36 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8265 (ptpt)
REVERT: C   91 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8144 (tt0)
REVERT: M   22 TRP cc_start: 0.3715 (OUTLIER) cc_final: 0.3371 (t-100)
REVERT: M   71 MET cc_start: 0.4983 (mmt) cc_final: 0.4327 (tpp)
REVERT: M  106 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7372 (tm)
REVERT: M  121 ASP cc_start: 0.7973 (t0) cc_final: 0.7630 (t70)
REVERT: M  248 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7686 (mm-30)
REVERT: M  278 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7613 (ptp90)
  outliers start: 44
  outliers final: 29
  residues processed: 209
  average time/residue: 0.7344
  time to fit residues: 167.8793
Evaluate side-chains
  213 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   18 HIS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain K residue   48 ILE
Chi-restraints excluded: chain K residue   61 ILE
Chi-restraints excluded: chain K residue  104 THR
Chi-restraints excluded: chain K residue  129 GLU
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  248 GLU
Chi-restraints excluded: chain K residue  255 GLU
Chi-restraints excluded: chain K residue  286 ASP
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain M residue   22 TRP
Chi-restraints excluded: chain M residue  106 LEU
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  248 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 163 optimal weight:    9.9990
   chunk 105 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   chunk 74 optimal weight:    0.3980
   chunk 139 optimal weight:   50.0000
   chunk 84 optimal weight:    4.9990
   chunk 133 optimal weight:    9.9990
   chunk 161 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 113 GLN
E  85 GLN
M 113 GLN
M 252 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.170116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.122215 restraints weight = 22604.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.24
r_work: 0.3155 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (14 function evaluations)
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091  19592  Z= 0.180
  Angle     :  0.699  14.846  27729  Z= 0.383
  Chirality :  0.049   0.252   3117
  Planarity :  0.005   0.088   2519
  Dihedral  : 28.341 160.538   4914
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.76 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.27 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 3.12 %
    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: -0.24 (0.22), residues: 1545
  helix:  0.65 (0.19), residues: 807
  sheet:  0.08 (0.48), residues: 140
  loop : -1.29 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  39 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.018   0.001   PHE K 223 
 TRP   0.013   0.002   TRP M  22 
 HIS   0.006   0.001   HIS F  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.18 (19592)
  covalent geometry    : angle       0.69884 /  0.38 (27729)
  hydrogen bonds       : bond        0.05795 /  3.81 (  831)
  hydrogen bonds       : angle       3.34357 /  2.29 ( 2108)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8291.28 seconds
wall clock time: 141 minutes 7.78 seconds (8467.78 seconds total)