Starting phenix.real_space_refine
on Sat Jul  4 17:57:40 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8du4_27715/07_2026/8du4_27715.map"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6774 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     292      5.49       5
     S      37      5.16       5
     C   10063      2.51       5
     N    3181      2.21       5
     O    3834      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 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: 17407
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'NLE:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 820
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 754
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 785
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'NLE:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "F"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 742
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "L"
      Number of atoms: 2382
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 303, 2350
          Classifications: {'peptide': 303}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 293}
      Conformer: "B"
        Number of residues, atoms: 303, 2350
          Classifications: {'peptide': 303}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2366
    Chain: "N"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2440
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 13, 'TRANS': 299}
    Chain: "O"
      Number of atoms: 597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 597
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   ASN L 225 " occ=0.00
      ... (6 atoms not shown)
      pdb=" ND2 ASN L 225 " occ=0.00
    residue:
      pdb=" N   LEU O  73 " occ=0.86
      ... (6 atoms not shown)
      pdb=" CD2 LEU O  73 " occ=0.86
    residue:
      pdb=" N   ARG O  74 " occ=0.87
      ... (9 atoms not shown)
      pdb=" NH2 ARG O  74 " occ=0.87
    residue:
      pdb=" N   GLY O  75 " occ=0.45
      ... (2 atoms not shown)
      pdb=" O   GLY O  75 " occ=0.45
  Time building chain proxies: 4.14, per 1000 atoms: 0.24
  Number of scatterers: 17407
  At special positions: 0
  Unit cell: (136.482, 128.018, 119.554, 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      37     16.00
     P     292     15.00
     O    3834      8.00
     N    3181      7.00
     C   10063      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: 1.30
  Conformation dependent library (CDL) restraints added in 602.9 milliseconds
  

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2718

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 21 sheets defined
      38.5% alpha, 14.9% beta
      145 base pairs and 222 stacking pairs defined.
    Time for finding SS restraints: 2.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 4.025A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.638A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 4.306A  pdb=" N   NLE A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.976A  pdb=" N   ILE A 124 " --> pdb=" O   NLE A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.604A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 76
      removed outlier: 3.926A  pdb=" N   ASN B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL B  65 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 4.003A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
      removed outlier: 4.015A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 74
      removed outlier: 3.902A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.745A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'D' and resid 35 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 4.154A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 120
      removed outlier: 3.705A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER D 120 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.541A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 77
    Processing helix  chain 'E' and resid 87 through 114
      removed outlier: 3.710A  pdb=" N   ALA E  91 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.732A  pdb=" N   ILE E 124 " --> pdb=" O   NLE E 120 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 4.011A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.761A  pdb=" N   ILE F  34 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 75
      removed outlier: 3.673A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 4.352A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 20
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 74
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 4.267A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 35 through 46
      removed outlier: 3.903A  pdb=" N   TYR H  39 " --> pdb=" O   ALA H  35 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   VAL H  45 " --> pdb=" O   VAL H  41 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.800A  pdb=" N   MET H  56 " --> pdb=" O   SER H  52 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 88 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.819A  pdb=" N   ALA H 121 " --> pdb=" O   CYS H 117 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 229 through 234
      removed outlier: 3.750A  pdb=" N   GLY N 234 " --> pdb=" O   ILE N 230 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 22 through 35
    Processing helix  chain 'O' and resid 37 through 41
    Processing helix  chain 'O' and resid 55 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.500A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.677A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102
      removed outlier: 7.374A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'L' and resid 36 through 37
      removed outlier: 4.407A  pdb=" N   LYS L 328 " --> pdb=" O   SER L 318 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   SER L 318 " --> pdb=" O   LYS L 328 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ASN L 314 " --> pdb=" O   SER L 332 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 50
      removed outlier: 3.672A  pdb=" N   SER L  50 " --> pdb=" O   SER L  63 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER L  64 " --> pdb=" O   LEU L  68 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   LEU L  68 " --> pdb=" O   SER L  64 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   ILE L  69 " --> pdb=" O   THR L  82 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   THR L  82 " --> pdb=" O   ILE L  69 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE L  71 " --> pdb=" O   GLU L  80 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 90 through 95
      removed outlier: 4.494A  pdb=" N   ASP L  92 " --> pdb=" O   ALA L 105 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 112 through 114
      removed outlier: 6.710A  pdb=" N   ILE L 113 " --> pdb=" O   LEU L 122 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 132 through 137
      removed outlier: 3.599A  pdb=" N   VAL L 145 " --> pdb=" O   ASN L 136 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ILE L 144 " --> pdb=" O   TRP L 156 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TRP L 156 " --> pdb=" O   ILE L 144 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS L 165 " --> pdb=" O   ILE L 155 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 179
      removed outlier: 3.862A  pdb=" N   HIS L 178 " --> pdb=" O   VAL L 187 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL L 187 " --> pdb=" O   HIS L 178 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG L 196 " --> pdb=" O   SER L 188 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   CYS L 195 " --> pdb=" O   THR L 208 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   THR L 208 " --> pdb=" O   CYS L 195 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ILE L 197 " --> pdb=" O   LEU L 206 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 228 through 233
      removed outlier: 4.085A  pdb=" N   THR L 237 " --> pdb=" O   THR L 233 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 264 through 267
      removed outlier: 4.056A  pdb=" N   GLN L 295 " --> pdb=" O   ILE L 285 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 16 through 18
      removed outlier: 4.260A  pdb=" N   ILE N 320 " --> pdb=" O   ASP N  18 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ALA N 311 " --> pdb=" O   VAL N 301 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   VAL N 301 " --> pdb=" O   ALA N 311 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ILE N 313 " --> pdb=" O   LEU N 299 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 38 through 42
      removed outlier: 6.559A  pdb=" N   ILE N  48 " --> pdb=" O   ILE N  61 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   ILE N  61 " --> pdb=" O   ILE N  48 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE N  50 " --> pdb=" O   ALA N  59 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'N' and resid 69 through 74
      removed outlier: 3.811A  pdb=" N   SER N  71 " --> pdb=" O   ALA N  84 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   SER N  83 " --> pdb=" O   SER N  91 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   SER N  91 " --> pdb=" O   SER N  83 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   GLN N 102 " --> pdb=" O   GLN N  92 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP N  94 " --> pdb=" O   CYS N 100 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   CYS N 100 " --> pdb=" O   ASP N  94 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'N' and resid 114 through 116
      removed outlier: 3.855A  pdb=" N   GLN N 114 " --> pdb=" O   LEU N 124 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   HIS N 116 " --> pdb=" O   LYS N 122 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   LYS N 122 " --> pdb=" O   HIS N 116 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'N' and resid 133 through 136
    Processing sheet with id=AB9, first strand: chain 'N' and resid 156 through 159
      removed outlier: 3.519A  pdb=" N   ALA N 187 " --> pdb=" O   VAL N 177 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 201 through 206
    Processing sheet with id=AC2, first strand: chain 'N' and resid 265 through 268
      removed outlier: 3.722A  pdb=" N   ILE N 278 " --> pdb=" O   LYS N 288 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LYS N 288 " --> pdb=" O   ILE N 278 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'O' and resid 12 through 16

    488 hydrogen bonds defined for protein.
    1410 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      371 hydrogen bonds
      738 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      222 stacking parallelities
  Total time for adding SS restraints: 3.28

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3899
        1.33 -     1.45: 4973
        1.45 -     1.57: 8833
        1.57 -     1.69: 582
        1.69 -     1.81: 48
  Bond restraints: 18335
  Sorted by residual:
  bond pdb=" C3'  DC I  84 "
       pdb=" C2'  DC I  84 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.28e+01
  bond pdb=" C3'  DG I  37 "
       pdb=" C2'  DG I  37 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DG I  67 "
       pdb=" C2'  DG I  67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.14e+01
  bond pdb=" C3'  DG J 286 "
       pdb=" C2'  DG J 286 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.86e+00
  bond pdb=" C3'  DG J 287 "
       pdb=" C2'  DG J 287 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.47e+00
  ... (remaining 18330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 25844
        2.75 -     5.51: 192
        5.51 -     8.26: 12
        8.26 -    11.01: 6
       11.01 -    13.77: 1
  Bond angle restraints: 26055
  Sorted by residual:
  angle pdb=" C   ASP N 149 "
        pdb=" CA  ASP N 149 "
        pdb=" CB  ASP N 149 "
      ideal   model   delta    sigma   weight residual
     117.23  109.76    7.47 1.36e+00 5.41e-01 3.02e+01
  angle pdb=" O4'  DA I  30 "
        pdb=" C4'  DA I  30 "
        pdb=" C3'  DA I  30 "
      ideal   model   delta    sigma   weight residual
     106.00  102.81    3.19 6.00e-01 2.78e+00 2.82e+01
  angle pdb=" CA  GLN F  27 "
        pdb=" CB  GLN F  27 "
        pdb=" CG  GLN F  27 "
      ideal   model   delta    sigma   weight residual
     114.10  124.30  -10.20 2.00e+00 2.50e-01 2.60e+01
  angle pdb=" O4'  DA I  49 "
        pdb=" C4'  DA I  49 "
        pdb=" C3'  DA I  49 "
      ideal   model   delta    sigma   weight residual
     106.00  103.10    2.90 6.00e-01 2.78e+00 2.34e+01
  angle pdb=" N3   DT I  27 "
        pdb=" C4   DT I  27 "
        pdb=" O4   DT I  27 "
      ideal   model   delta    sigma   weight residual
     119.90  122.59   -2.69 6.00e-01 2.78e+00 2.02e+01
  ... (remaining 26050 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.05: 8661
       33.05 -    66.10: 1559
       66.10 -    99.15: 46
       99.15 -   132.20: 2
      132.20 -   165.25: 1
  Dihedral angle restraints: 10269
    sinusoidal: 6058
      harmonic: 4211
  Sorted by residual:
  dihedral pdb=" CA  ASN H  81 "
           pdb=" C   ASN H  81 "
           pdb=" N   LYS H  82 "
           pdb=" CA  LYS H  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.72   22.28     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" C4'  DG J 244 "
           pdb=" C3'  DG J 244 "
           pdb=" O3'  DG J 244 "
           pdb=" P    DG J 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.75  165.25     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" CA  LEU G  33 "
           pdb=" C   LEU G  33 "
           pdb=" N   LEU G  34 "
           pdb=" CA  LEU G  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 10266 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 2338
       0.053 -    0.106: 558
       0.106 -    0.159: 71
       0.159 -    0.211: 3
       0.211 -    0.264: 2
  Chirality restraints: 2972
  Sorted by residual:
  chirality pdb=" CG  LEU L 240 "
            pdb=" CB  LEU L 240 "
            pdb=" CD1 LEU L 240 "
            pdb=" CD2 LEU L 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.85    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  MET H  59 "
            pdb=" N   MET H  59 "
            pdb=" C   MET H  59 "
            pdb=" CB  MET H  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CG  LEU N 178 "
            pdb=" CB  LEU N 178 "
            pdb=" CD1 LEU N 178 "
            pdb=" CD2 LEU N 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 2969 not shown)

  Planarity restraints: 2279
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN F  27 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.95e+00
        pdb=" C   GLN F  27 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLN F  27 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLY F  28 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  54 "   -0.014 2.00e-02 2.50e+03   1.79e-02 7.21e+00
        pdb=" N1   DC I  54 "    0.020 2.00e-02 2.50e+03
        pdb=" C2   DC I  54 "   -0.039 2.00e-02 2.50e+03
        pdb=" O2   DC I  54 "    0.027 2.00e-02 2.50e+03
        pdb=" N3   DC I  54 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DC I  54 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC I  54 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DC I  54 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC I  54 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.043 5.00e-02 4.00e+02   6.57e-02 6.90e+00
        pdb=" N   PRO E  43 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.036 5.00e-02 4.00e+02
  ... (remaining 2276 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 552
        2.67 -     3.23: 15706
        3.23 -     3.79: 30493
        3.79 -     4.34: 38759
        4.34 -     4.90: 57661
  Nonbonded interactions: 143171
  Sorted by model distance:
  nonbonded pdb=" OH  TYR L 252 "
            pdb=" O   LEU L 288 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" NE2 GLN G  84 "
            pdb=" O   GLY G 106 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG1 THR N 217 "
            pdb=" OD1 ASP N 219 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" O   ALA E  75 "
            pdb=" N   LYS E  79 "
     model   vdw
     2.172 3.120
  ... (remaining 143166 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 40 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 23 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 15 through 117)
  selection = (chain 'G' and resid 15 through 117)
}
ncs_group {
  reference = (chain 'D' and resid 28 through 121)
  selection = (chain 'H' and resid 28 through 121)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.850
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5231
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  18335  Z= 0.445
  Angle     :  0.797  13.768  26055  Z= 0.633
  Chirality :  0.045   0.264   2972
  Planarity :  0.005   0.066   2279
  Dihedral  : 25.341 165.255   7551
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.22 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.22), residues: 1418
  helix: -0.14 (0.23), residues: 515
  sheet: -1.40 (0.36), residues: 212
  loop : -2.19 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  40 
 TYR   0.017   0.002   TYR E  54 
 PHE   0.017   0.002   PHE E  67 
 TRP   0.020   0.002   TRP N  74 
 HIS   0.025   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00520 /  0.45 (18335)
  covalent geometry    : angle       0.79697 /  0.63 (26055)
  hydrogen bonds       : bond        0.11928 /  7.97 (  859)
  hydrogen bonds       : angle       5.72708 /  4.06 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8223 (mt)
REVERT: A   54 TYR cc_start: 0.8741 (m-80) cc_final: 0.8446 (m-10)
REVERT: H   93 THR cc_start: 0.7300 (t) cc_final: 0.4729 (p)
REVERT: L  182 ASP cc_start: 0.2575 (m-30) cc_final: 0.1098 (t70)
REVERT: N  166 ILE cc_start: -0.1510 (OUTLIER) cc_final: -0.1986 (mm)
  outliers start: 21
  outliers final: 10
  residues processed: 114
  average time/residue: 0.1618
  time to fit residues: 26.8869
Evaluate side-chains
  87 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain N residue  166 ILE
Chi-restraints excluded: chain N residue  222 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    5.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  93 GLN
L 130 ASN
N 183 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.242262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.209804 restraints weight = 63961.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.207478 restraints weight = 76130.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.205021 restraints weight = 62629.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.204720 restraints weight = 53864.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.204239 restraints weight = 47042.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.4422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4423 r_free = 0.4423    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4422 r_free = 0.4422    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (11 function evaluations)
r_final: 0.4422
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6256
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.123  18335  Z= 0.495
  Angle     :  1.275  17.390  26055  Z= 0.675
  Chirality :  0.074   0.487   2972
  Planarity :  0.011   0.099   2279
  Dihedral  : 30.233 179.513   4809
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.48 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 17.11 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.95 (0.20), residues: 1418
  helix: -1.48 (0.20), residues: 508
  sheet: -1.11 (0.39), residues: 186
  loop : -2.59 (0.21), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.002   ARG A 129 
 TYR   0.057   0.006   TYR B  98 
 PHE   0.039   0.004   PHE H  62 
 TRP   0.015   0.003   TRP L 114 
 HIS   0.019   0.004   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01128 /  0.49 (18335)
  covalent geometry    : angle       1.27517 /  0.67 (26055)
  hydrogen bonds       : bond        0.13055 /  8.76 (  859)
  hydrogen bonds       : angle       6.16880 /  4.53 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 78
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7630 (ttp-110)
REVERT: A   93 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8928 (tt0)
REVERT: A  131 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8439 (ttp80)
REVERT: E   50 GLU cc_start: 0.7922 (pt0) cc_final: 0.7508 (pt0)
REVERT: H   34 TYR cc_start: 0.1297 (OUTLIER) cc_final: 0.0697 (m-10)
REVERT: L  130 ASN cc_start: 0.3089 (OUTLIER) cc_final: 0.2066 (t0)
REVERT: L  182 ASP cc_start: 0.2601 (m-30) cc_final: 0.1512 (t70)
REVERT: N   65 HIS cc_start: 0.3658 (OUTLIER) cc_final: 0.3252 (m90)
REVERT: N  167 TYR cc_start: 0.2568 (OUTLIER) cc_final: 0.1514 (m-10)
REVERT: N  259 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5934 (t80)
  outliers start: 86
  outliers final: 40
  residues processed: 156
  average time/residue: 0.1470
  time to fit residues: 34.0443
Evaluate side-chains
  118 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 70
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   34 TYR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   85 THR
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain L residue  130 ASN
Chi-restraints excluded: chain L residue  155 ILE
Chi-restraints excluded: chain L residue  293 ILE
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   74 TRP
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  155 VAL
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  320 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 163 optimal weight:   10.0000
   chunk 145 optimal weight:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 112 optimal weight:   30.0000
   chunk 113 optimal weight:   10.0000
   chunk 134 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 143 optimal weight:    0.7980
   chunk 160 optimal weight:   20.0000
   overall best weight:    1.5582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.246193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.225958 restraints weight = 66141.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.228571 restraints weight = 86332.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.230243 restraints weight = 28853.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.230256 restraints weight = 15708.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.230256 restraints weight = 15539.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.4669
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4669 r_free = 0.4669    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4669 r_free = 0.4669    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5692
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  18335  Z= 0.200
  Angle     :  0.765  10.654  26055  Z= 0.428
  Chirality :  0.052   0.324   2972
  Planarity :  0.006   0.104   2279
  Dihedral  : 30.067 173.621   4797
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 19.94 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.21), residues: 1418
  helix: -0.47 (0.22), residues: 512
  sheet: -1.14 (0.40), residues: 180
  loop : -2.43 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 129 
 TYR   0.024   0.002   TYR H  39 
 PHE   0.019   0.002   PHE N 213 
 TRP   0.013   0.001   TRP L 286 
 HIS   0.012   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.20 (18335)
  covalent geometry    : angle       0.76457 /  0.43 (26055)
  hydrogen bonds       : bond        0.07360 /  4.94 (  859)
  hydrogen bonds       : angle       4.92423 /  3.59 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 84
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8590 (tt0)
REVERT: E   65 LEU cc_start: 0.7736 (tp) cc_final: 0.7309 (tp)
REVERT: E   83 ARG cc_start: 0.1925 (OUTLIER) cc_final: 0.1488 (mtp-110)
REVERT: H   58 ILE cc_start: 0.6565 (OUTLIER) cc_final: 0.6299 (tt)
REVERT: N  167 TYR cc_start: 0.2514 (OUTLIER) cc_final: 0.1530 (m-10)
REVERT: N  259 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5725 (t80)
  outliers start: 56
  outliers final: 32
  residues processed: 132
  average time/residue: 0.1486
  time to fit residues: 28.9089
Evaluate side-chains
  112 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 75
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   83 ARG
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue  240 LEU
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  286 LEU
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain O residue   69 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 37 optimal weight:    0.7980
   chunk 92 optimal weight:   10.0000
   chunk 115 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 160 optimal weight:   20.0000
   chunk 138 optimal weight:   10.0000
   chunk 71 optimal weight:   40.0000
   chunk 7 optimal weight:    0.2980
   overall best weight:    2.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 130 ASN
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.241098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.210857 restraints weight = 78046.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.208853 restraints weight = 84128.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.207293 restraints weight = 62830.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.207384 restraints weight = 60214.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.207335 restraints weight = 43847.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.4449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4449 r_free = 0.4449    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4449 r_free = 0.4449    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6253
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072  18335  Z= 0.293
  Angle     :  0.888  10.025  26055  Z= 0.486
  Chirality :  0.057   0.329   2972
  Planarity :  0.007   0.085   2279
  Dihedral  : 30.118 178.535   4797
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 17.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 18.48 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.21), residues: 1418
  helix: -0.67 (0.22), residues: 521
  sheet: -0.91 (0.40), residues: 191
  loop : -2.50 (0.21), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG H  83 
 TYR   0.039   0.003   TYR D  80 
 PHE   0.038   0.002   PHE A  84 
 TRP   0.012   0.002   TRP L 286 
 HIS   0.018   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00653 /  0.29 (18335)
  covalent geometry    : angle       0.88759 /  0.49 (26055)
  hydrogen bonds       : bond        0.09349 /  6.24 (  859)
  hydrogen bonds       : angle       5.18406 /  3.81 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 82
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8823 (tt0)
REVERT: A   94 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7398 (mt-10)
REVERT: A  131 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8403 (ttp80)
REVERT: C   95 LYS cc_start: 0.8613 (tppt) cc_final: 0.8385 (mmmt)
REVERT: D   98 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8594 (mp)
REVERT: E   83 ARG cc_start: 0.1689 (OUTLIER) cc_final: 0.1220 (mtp-110)
REVERT: H   34 TYR cc_start: 0.1470 (OUTLIER) cc_final: 0.0655 (m-10)
REVERT: H   56 MET cc_start: 0.5614 (pmm) cc_final: 0.5330 (pmm)
REVERT: H   79 HIS cc_start: 0.1128 (OUTLIER) cc_final: 0.0307 (t70)
REVERT: L  130 ASN cc_start: 0.3322 (OUTLIER) cc_final: 0.2763 (t0)
REVERT: N   65 HIS cc_start: 0.3556 (OUTLIER) cc_final: 0.3103 (m90)
REVERT: N  166 ILE cc_start: -0.1120 (OUTLIER) cc_final: -0.1788 (mm)
REVERT: N  167 TYR cc_start: 0.2480 (OUTLIER) cc_final: 0.1491 (m-10)
REVERT: N  259 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5740 (t80)
  outliers start: 85
  outliers final: 53
  residues processed: 156
  average time/residue: 0.1428
  time to fit residues: 32.6587
Evaluate side-chains
  131 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 66
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   35 ARG
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   83 ARG
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   34 TYR
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   79 HIS
Chi-restraints excluded: chain H residue   85 THR
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain L residue   88 LEU
Chi-restraints excluded: chain L residue  130 ASN
Chi-restraints excluded: chain L residue  155 ILE
Chi-restraints excluded: chain L residue  293 ILE
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   74 TRP
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  166 ILE
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  186 VAL
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  266 ILE
Chi-restraints excluded: chain N residue  286 LEU
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 124 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 78 optimal weight:   10.0000
   chunk 152 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 128 optimal weight:    8.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    3.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 130 ASN
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.237141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.206959 restraints weight = 74019.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.206060 restraints weight = 80222.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.203883 restraints weight = 57739.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.203644 restraints weight = 57249.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.203426 restraints weight = 42954.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4444 r_free = 0.4444    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4443 r_free = 0.4443    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (12 function evaluations)
r_final: 0.4443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6308
moved from start:          0.4984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.175  18335  Z= 0.305
  Angle     :  0.870  13.028  26055  Z= 0.476
  Chirality :  0.056   0.304   2972
  Planarity :  0.007   0.059   2279
  Dihedral  : 30.155 176.325   4797
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 19.94 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.39 (0.21), residues: 1418
  helix: -0.66 (0.22), residues: 521
  sheet: -1.15 (0.37), residues: 213
  loop : -2.50 (0.22), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  83 
 TYR   0.032   0.003   TYR F  88 
 PHE   0.031   0.002   PHE A  84 
 TRP   0.013   0.001   TRP L 286 
 HIS   0.016   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00690 /  0.31 (18335)
  covalent geometry    : angle       0.86957 /  0.48 (26055)
  hydrogen bonds       : bond        0.08481 /  5.65 (  859)
  hydrogen bonds       : angle       5.23711 /  3.83 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 78
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8777 (tt0)
REVERT: A  131 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8389 (ttp80)
REVERT: C   95 LYS cc_start: 0.8577 (tppt) cc_final: 0.8353 (mmmt)
REVERT: D   98 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8545 (mp)
REVERT: E   83 ARG cc_start: 0.1756 (OUTLIER) cc_final: 0.1444 (mtp-110)
REVERT: H   34 TYR cc_start: 0.1216 (OUTLIER) cc_final: 0.0584 (m-10)
REVERT: H   58 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7483 (mt)
REVERT: N   65 HIS cc_start: 0.3750 (OUTLIER) cc_final: 0.3424 (m90)
REVERT: N  167 TYR cc_start: 0.2540 (OUTLIER) cc_final: 0.1431 (m-10)
REVERT: N  259 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5373 (t80)
  outliers start: 86
  outliers final: 48
  residues processed: 155
  average time/residue: 0.1411
  time to fit residues: 32.4792
Evaluate side-chains
  127 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 70
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   83 ARG
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   34 TYR
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain L residue   88 LEU
Chi-restraints excluded: chain L residue  113 ILE
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   chunk 158 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 118 optimal weight:    8.9990
   chunk 130 optimal weight:    9.9990
   chunk 49 optimal weight:    0.5980
   chunk 157 optimal weight:    0.0270
   chunk 55 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 170 ASN
O  40 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.241683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.212286 restraints weight = 77932.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.210620 restraints weight = 79068.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.208579 restraints weight = 56971.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.208749 restraints weight = 56417.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.208688 restraints weight = 39531.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.4486
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4487 r_free = 0.4487    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4486 r_free = 0.4486    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.4486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6188
moved from start:          0.4978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18335  Z= 0.151
  Angle     :  0.665  10.900  26055  Z= 0.377
  Chirality :  0.048   0.302   2972
  Planarity :  0.005   0.055   2279
  Dihedral  : 29.845 176.882   4793
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 22.60 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.22), residues: 1418
  helix:  0.02 (0.22), residues: 526
  sheet: -1.00 (0.38), residues: 216
  loop : -2.28 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  83 
 TYR   0.022   0.002   TYR L 131 
 PHE   0.019   0.001   PHE N 213 
 TRP   0.017   0.001   TRP L 286 
 HIS   0.015   0.001   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 (18335)
  covalent geometry    : angle       0.66541 /  0.38 (26055)
  hydrogen bonds       : bond        0.06334 /  4.25 (  859)
  hydrogen bonds       : angle       4.48064 /  3.26 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 87
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8346 (tt0)
REVERT: A   93 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8323 (tt0)
REVERT: A  131 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8145 (ttp80)
REVERT: D   98 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8388 (mp)
REVERT: E   83 ARG cc_start: 0.0410 (OUTLIER) cc_final: 0.0169 (mtp85)
REVERT: L  130 ASN cc_start: 0.3948 (m-40) cc_final: 0.3599 (t0)
REVERT: N  259 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5433 (t80)
  outliers start: 53
  outliers final: 34
  residues processed: 132
  average time/residue: 0.1546
  time to fit residues: 29.9537
Evaluate side-chains
  118 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 78
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   83 ARG
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  186 VAL
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 136 optimal weight:   30.0000
   chunk 149 optimal weight:    7.9990
   chunk 141 optimal weight:    0.9990
   chunk 156 optimal weight:    8.9990
   chunk 86 optimal weight:   30.0000
   chunk 0 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 148 optimal weight:    0.7980
   overall best weight:    2.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.236195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.214137 restraints weight = 62514.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.217132 restraints weight = 83527.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.218224 restraints weight = 27284.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.218861 restraints weight = 16896.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.219073 restraints weight = 14296.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4550 r_free = 0.4550    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4550 r_free = 0.4550    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6040
moved from start:          0.5413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  18335  Z= 0.245
  Angle     :  0.767   9.892  26055  Z= 0.422
  Chirality :  0.052   0.264   2972
  Planarity :  0.006   0.053   2279
  Dihedral  : 29.892 176.965   4791
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 21.79 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.22), residues: 1418
  helix: -0.05 (0.22), residues: 521
  sheet: -0.95 (0.37), residues: 227
  loop : -2.34 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  83 
 TYR   0.027   0.002   TYR H  39 
 PHE   0.022   0.002   PHE A  84 
 TRP   0.012   0.001   TRP L 286 
 HIS   0.019   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.25 (18335)
  covalent geometry    : angle       0.76652 /  0.42 (26055)
  hydrogen bonds       : bond        0.07830 /  5.21 (  859)
  hydrogen bonds       : angle       4.77018 /  3.49 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 75
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8266 (tt0)
REVERT: A   93 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8661 (tt0)
REVERT: A  131 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8156 (ttp80)
REVERT: C   74 LYS cc_start: 0.7978 (mppt) cc_final: 0.7323 (mmtp)
REVERT: C   95 LYS cc_start: 0.8613 (tppt) cc_final: 0.8274 (tptp)
REVERT: D   98 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8446 (mp)
REVERT: N   65 HIS cc_start: 0.3613 (OUTLIER) cc_final: 0.3287 (m90)
REVERT: N  259 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5463 (t80)
  outliers start: 63
  outliers final: 43
  residues processed: 131
  average time/residue: 0.1277
  time to fit residues: 25.2235
Evaluate side-chains
  125 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 76
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   35 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 98 optimal weight:   20.0000
   chunk 66 optimal weight:    0.5980
   chunk 110 optimal weight:    9.9990
   chunk 71 optimal weight:   40.0000
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 153 optimal weight:    8.9990
   chunk 147 optimal weight:    0.8980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.240013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.219130 restraints weight = 74593.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.222119 restraints weight = 82961.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.223845 restraints weight = 26307.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.224545 restraints weight = 14687.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.224654 restraints weight = 10119.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.4610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4611 r_free = 0.4611    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4610 r_free = 0.4610    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.4610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5918
moved from start:          0.5492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  18335  Z= 0.146
  Angle     :  0.637   9.792  26055  Z= 0.362
  Chirality :  0.046   0.241   2972
  Planarity :  0.004   0.053   2279
  Dihedral  : 29.730 176.263   4791
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 22.84 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.22), residues: 1418
  helix:  0.38 (0.22), residues: 528
  sheet: -0.84 (0.36), residues: 232
  loop : -2.24 (0.23), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  83 
 TYR   0.012   0.001   TYR F  88 
 PHE   0.017   0.001   PHE N 213 
 TRP   0.016   0.001   TRP L 286 
 HIS   0.016   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.15 (18335)
  covalent geometry    : angle       0.63684 /  0.36 (26055)
  hydrogen bonds       : bond        0.06129 /  4.12 (  859)
  hydrogen bonds       : angle       4.29576 /  3.13 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 80
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8357 (tt0)
REVERT: A   93 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8467 (tt0)
REVERT: A  131 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8048 (ttp80)
REVERT: C   74 LYS cc_start: 0.7841 (mppt) cc_final: 0.7424 (mmtp)
REVERT: L  107 ASP cc_start: 0.3254 (m-30) cc_final: 0.1959 (t0)
REVERT: N   65 HIS cc_start: 0.3398 (OUTLIER) cc_final: 0.3145 (m90)
REVERT: N  259 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5466 (t80)
  outliers start: 46
  outliers final: 32
  residues processed: 120
  average time/residue: 0.1524
  time to fit residues: 27.0860
Evaluate side-chains
  114 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 77
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  186 VAL
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  287 VAL
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    5 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 143 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 151 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.239859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.210116 restraints weight = 77599.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.208344 restraints weight = 80271.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.206669 restraints weight = 59440.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.206620 restraints weight = 49148.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.206180 restraints weight = 42710.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.4480
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4480 r_free = 0.4480    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4480 r_free = 0.4480    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.4480
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6227
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  18335  Z= 0.145
  Angle     :  0.634   9.636  26055  Z= 0.358
  Chirality :  0.045   0.222   2972
  Planarity :  0.004   0.050   2279
  Dihedral  : 29.658 176.580   4789
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.08 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.22), residues: 1418
  helix:  0.61 (0.22), residues: 530
  sheet: -0.76 (0.37), residues: 227
  loop : -2.22 (0.23), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  69 
 TYR   0.012   0.001   TYR N 225 
 PHE   0.017   0.001   PHE N 213 
 TRP   0.014   0.001   TRP L 286 
 HIS   0.012   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.14 (18335)
  covalent geometry    : angle       0.63351 /  0.36 (26055)
  hydrogen bonds       : bond        0.06044 /  4.03 (  859)
  hydrogen bonds       : angle       4.20374 /  3.06 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 76
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8552 (tt0)
REVERT: A  131 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8135 (ttp80)
REVERT: C   61 GLU cc_start: 0.8205 (tp30) cc_final: 0.7928 (tp30)
REVERT: H  105 LYS cc_start: 0.7834 (mptt) cc_final: 0.7172 (pptt)
REVERT: L  107 ASP cc_start: 0.3285 (m-30) cc_final: 0.1985 (t0)
REVERT: N   65 HIS cc_start: 0.3413 (OUTLIER) cc_final: 0.2906 (m90)
REVERT: N  259 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5516 (t80)
  outliers start: 42
  outliers final: 32
  residues processed: 114
  average time/residue: 0.1543
  time to fit residues: 26.0119
Evaluate side-chains
  112 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 76
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  186 VAL
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  287 VAL
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 112 optimal weight:    8.9990
   chunk 144 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 87 optimal weight:   20.0000
   chunk 3 optimal weight:    0.8980
   chunk 116 optimal weight:    0.1980
   chunk 47 optimal weight:    2.9990
   chunk 114 optimal weight:    4.9990
   chunk 132 optimal weight:    0.8980
   chunk 72 optimal weight:   30.0000
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  81 ASN
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4830 r_free = 0.4830 target = 0.239309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.209859 restraints weight = 78020.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.208685 restraints weight = 86593.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.207600 restraints weight = 50641.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.206520 restraints weight = 52955.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.205856 restraints weight = 47376.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4463 r_free = 0.4463    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4463 r_free = 0.4463    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6235
moved from start:          0.5862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  18335  Z= 0.142
  Angle     :  0.616   9.599  26055  Z= 0.350
  Chirality :  0.044   0.224   2972
  Planarity :  0.004   0.049   2279
  Dihedral  : 29.569 176.401   4789
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.41 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.22), residues: 1418
  helix:  0.92 (0.23), residues: 518
  sheet: -0.73 (0.36), residues: 241
  loop : -2.21 (0.23), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  78 
 TYR   0.010   0.001   TYR F  88 
 PHE   0.018   0.001   PHE E  84 
 TRP   0.013   0.001   TRP L 286 
 HIS   0.013   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.14 (18335)
  covalent geometry    : angle       0.61630 /  0.35 (26055)
  hydrogen bonds       : bond        0.05732 /  3.84 (  859)
  hydrogen bonds       : angle       4.07291 /  2.96 ( 2148)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 80
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8108 (ttp80)
REVERT: C   74 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8141 (mmtm)
REVERT: L  107 ASP cc_start: 0.3037 (m-30) cc_final: 0.1786 (t0)
REVERT: N   65 HIS cc_start: 0.3459 (OUTLIER) cc_final: 0.2919 (m90)
REVERT: N  259 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5427 (t80)
  outliers start: 39
  outliers final: 30
  residues processed: 115
  average time/residue: 0.1588
  time to fit residues: 26.7023
Evaluate side-chains
  112 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  186 VAL
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  287 VAL
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0670
   chunk 27 optimal weight:    0.0050
   chunk 148 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 91 optimal weight:    9.9990
   overall best weight:    0.5132

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
H 106 HIS
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.240318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.219461 restraints weight = 66183.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.222330 restraints weight = 84385.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.223643 restraints weight = 26113.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.224413 restraints weight = 15587.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.224559 restraints weight = 11200.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.4613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4613 r_free = 0.4613    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4612 r_free = 0.4612    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (11 function evaluations)
r_final: 0.4612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5895
moved from start:          0.5943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  18335  Z= 0.130
  Angle     :  0.604  12.669  26055  Z= 0.341
  Chirality :  0.044   0.220   2972
  Planarity :  0.004   0.048   2279
  Dihedral  : 29.496 176.423   4789
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.24 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.23), residues: 1418
  helix:  1.12 (0.23), residues: 519
  sheet: -0.72 (0.36), residues: 241
  loop : -2.15 (0.23), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG O  72 
 TYR   0.015   0.001   TYR N 225 
 PHE   0.016   0.001   PHE N 213 
 TRP   0.013   0.001   TRP L 286 
 HIS   0.014   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.13 (18335)
  covalent geometry    : angle       0.60358 /  0.34 (26055)
  hydrogen bonds       : bond        0.05436 /  3.64 (  859)
  hydrogen bonds       : angle       3.96624 /  2.89 ( 2148)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2537.74 seconds
wall clock time: 44 minutes 57.33 seconds (2697.33 seconds total)