Starting phenix.real_space_refine
on Sun Sep 13 09:52:44 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8du4_27715/09_2026/8du4_27715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8du4_27715/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8du4_27715/09_2026/8du4_27715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8du4_27715/09_2026/8du4_27715.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8du4_27715/09_2026/8du4_27715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8du4_27715/09_2026/8du4_27715.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8du4_27715/09_2026/8du4_27715.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8du4_27715/09_2026/8du4_27715.cif"
  }
  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-2.2.1-6174/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: 3.86, per 1000 atoms: 0.22
  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: 1.68
  Conformation dependent library (CDL) restraints added in 674.1 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: 2.27
  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: 3.35

  Time building geometry restraints manager: 2.19 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:             2.120
  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:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     18.430
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.430
-------------------------------------------------------------------------------
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= 0.446
  Angle     :  0.802  13.768  26055  Z= 0.638
  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       0.80159 /  0.64 (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  : 0.492 
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: 0.1658
  time to fit residues: 27.4220
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  : 0.484 
-------------------------------------------------------------------------------
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:   10.0000
   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 = 0.4838 r_free = 0.4838 target = 0.241794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.209447 restraints weight = 63737.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.207234 restraints weight = 76339.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.204911 restraints weight = 63718.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.204731 restraints weight = 54901.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.204303 restraints weight = 50380.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4422
|-occupancy refinement: start-------------------------------------------------|
| 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:       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:       40 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (8 function evaluations)
r_final: 0.4422
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6263
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.132  18335  Z= 0.531
  Angle     :  1.311  18.282  26055  Z= 0.693
  Chirality :  0.077   0.542   2972
  Planarity :  0.011   0.103   2279
  Dihedral  : 30.224 178.567   4809
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 23.33
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 10.62 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 17.03 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.20), residues: 1418
  helix: -1.55 (0.20), residues: 510
  sheet: -1.18 (0.38), residues: 197
  loop : -2.65 (0.21), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG A 129 
 TYR   0.062   0.006   TYR B  98 
 PHE   0.039   0.005   PHE H  62 
 TRP   0.016   0.003   TRP L 114 
 HIS   0.021   0.004   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01210 /  0.53 (18335)
  covalent geometry    : angle       1.31053 /  0.69 (26055)
  hydrogen bonds       : bond        0.13477 /  9.05 (  859)
  hydrogen bonds       : angle       6.26109 /  4.60 ( 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
  172 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 81
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7595 (ttp-110)
REVERT: A   93 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8915 (tt0)
REVERT: A  131 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8493 (ttp80)
REVERT: B   35 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8079 (mmt90)
REVERT: E   50 GLU cc_start: 0.7936 (pt0) cc_final: 0.7545 (pt0)
REVERT: H   34 TYR cc_start: 0.1441 (OUTLIER) cc_final: 0.0801 (m-10)
REVERT: L  130 ASN cc_start: 0.3119 (OUTLIER) cc_final: 0.2090 (t0)
REVERT: L  182 ASP cc_start: 0.2643 (m-30) cc_final: 0.1526 (t70)
REVERT: N   65 HIS cc_start: 0.3706 (OUTLIER) cc_final: 0.3267 (m90)
REVERT: N  167 TYR cc_start: 0.2632 (OUTLIER) cc_final: 0.1535 (m-10)
REVERT: N  259 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.5927 (t80)
  outliers start: 91
  outliers final: 44
  residues processed: 165
  average time/residue: 0.1507
  time to fit residues: 37.0135
Evaluate side-chains
  122 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 69
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
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   77 ASP
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   35 ARG
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   63 LEU
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   64 GLU
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 H residue  103 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   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:    6.9990
   chunk 163 optimal weight:    6.9990
   chunk 145 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 112 optimal weight:    8.9990
   chunk 113 optimal weight:    8.9990
   chunk 134 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 143 optimal weight:    7.9990
   chunk 160 optimal weight:    3.9990
   overall best weight:    1.3782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** 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 = 0.4887 r_free = 0.4887 target = 0.246273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.225983 restraints weight = 66160.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.228631 restraints weight = 87390.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.230559 restraints weight = 29549.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.230559 restraints weight = 15288.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.230559 restraints weight = 15288.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.4672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4672 r_free = 0.4672    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4671 r_free = 0.4671    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)
r_final: 0.4671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5697
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  18335  Z= 0.195
  Angle     :  0.771  10.374  26055  Z= 0.430
  Chirality :  0.052   0.327   2972
  Planarity :  0.006   0.116   2279
  Dihedral  : 30.017 172.830   4797
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 20.34 %
    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: -2.28 (0.21), residues: 1418
  helix: -0.49 (0.22), residues: 512
  sheet: -1.12 (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 L 131 
 PHE   0.020   0.002   PHE N 213 
 TRP   0.013   0.001   TRP L 286 
 HIS   0.011   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.20 (18335)
  covalent geometry    : angle       0.77077 /  0.43 (26055)
  hydrogen bonds       : bond        0.07316 /  4.92 (  859)
  hydrogen bonds       : angle       4.90194 /  3.58 ( 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
  134 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 83
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8580 (tt0)
REVERT: E   65 LEU cc_start: 0.7865 (tp) cc_final: 0.7462 (mt)
REVERT: E   83 ARG cc_start: 0.1748 (OUTLIER) cc_final: 0.1374 (mtp-110)
REVERT: H   58 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6435 (tt)
REVERT: N  167 TYR cc_start: 0.2518 (OUTLIER) cc_final: 0.1529 (m-10)
REVERT: N  259 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5735 (t80)
REVERT: O   15 LEU cc_start: 0.0411 (OUTLIER) cc_final: -0.1544 (tp)
  outliers start: 51
  outliers final: 29
  residues processed: 127
  average time/residue: 0.1603
  time to fit residues: 29.9126
Evaluate side-chains
  111 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
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  102 ILE
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   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   79 ILE
Chi-restraints excluded: chain H residue   36 ILE
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 L residue  240 LEU
Chi-restraints excluded: chain N residue   66 ILE
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   15 LEU
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:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   chunk 115 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   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:   30.0000
   chunk 7 optimal weight:    0.1980
   overall best weight:    2.5984

-------------------------------------------------------------------------------
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**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.242061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.211106 restraints weight = 78033.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.209096 restraints weight = 79331.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.207050 restraints weight = 60579.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.207126 restraints weight = 54290.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.206768 restraints weight = 42808.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4447 r_free = 0.4447    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4447 r_free = 0.4447    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6253
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.097  18335  Z= 0.289
  Angle     :  0.866   9.349  26055  Z= 0.471
  Chirality :  0.056   0.294   2972
  Planarity :  0.007   0.089   2279
  Dihedral  : 30.006 177.290   4795
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 19.37 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.25 (0.21), residues: 1418
  helix: -0.51 (0.22), residues: 521
  sheet: -1.00 (0.39), residues: 198
  loop : -2.47 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG N 103 
 TYR   0.030   0.003   TYR D  80 
 PHE   0.033   0.002   PHE A  84 
 TRP   0.030   0.002   TRP N  93 
 HIS   0.016   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00646 /  0.29 (18335)
  covalent geometry    : angle       0.86594 /  0.47 (26055)
  hydrogen bonds       : bond        0.08779 /  5.87 (  859)
  hydrogen bonds       : angle       5.09307 /  3.75 ( 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
  155 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 78
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8645 (tt0)
REVERT: A  131 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8218 (ttp80)
REVERT: C   95 LYS cc_start: 0.8533 (tppt) cc_final: 0.8318 (mmmt)
REVERT: D   98 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8631 (mp)
REVERT: E   83 ARG cc_start: 0.1649 (OUTLIER) cc_final: 0.1140 (mtp-110)
REVERT: H   34 TYR cc_start: 0.1308 (OUTLIER) cc_final: 0.0461 (m-10)
REVERT: H   56 MET cc_start: 0.5120 (OUTLIER) cc_final: 0.3743 (ptp)
REVERT: L  130 ASN cc_start: 0.3303 (OUTLIER) cc_final: 0.2611 (t0)
REVERT: N   65 HIS cc_start: 0.3601 (OUTLIER) cc_final: 0.3199 (m90)
REVERT: N  166 ILE cc_start: -0.1141 (OUTLIER) cc_final: -0.1799 (mm)
REVERT: N  167 TYR cc_start: 0.2551 (OUTLIER) cc_final: 0.1499 (m-10)
REVERT: N  259 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5679 (t80)
  outliers start: 77
  outliers final: 48
  residues processed: 146
  average time/residue: 0.1490
  time to fit residues: 32.5465
Evaluate side-chains
  128 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 69
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
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   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   83 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  102 ILE
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   61 LEU
Chi-restraints excluded: chain E residue   83 ARG
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 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   45 VAL
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue   88 LEU
Chi-restraints excluded: chain L residue  130 ASN
Chi-restraints excluded: chain L residue  293 ILE
Chi-restraints excluded: chain L residue  301 THR
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  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  286 LEU
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain O residue    9 THR
Chi-restraints excluded: chain O residue   15 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 78 optimal weight:    9.9990
   chunk 152 optimal weight:    8.9990
   chunk 60 optimal weight:    0.7980
   chunk 130 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 128 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   overall best weight:    3.3184

-------------------------------------------------------------------------------
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
F  25 ASN
H  46 HIS
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 170 ASN
O  40 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.236789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.206111 restraints weight = 73890.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.205103 restraints weight = 80550.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.203220 restraints weight = 59370.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.202634 restraints weight = 58181.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.201736 restraints weight = 49136.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4424 r_free = 0.4424    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4425 r_free = 0.4425    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.4425
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6359
moved from start:          0.5052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.096  18335  Z= 0.314
  Angle     :  0.913  16.762  26055  Z= 0.497
  Chirality :  0.058   0.305   2972
  Planarity :  0.008   0.121   2279
  Dihedral  : 30.082 176.004   4795
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 20.34 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.46 (0.21), residues: 1418
  helix: -0.72 (0.21), residues: 521
  sheet: -1.15 (0.37), residues: 212
  loop : -2.56 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  72 
 TYR   0.034   0.003   TYR F  88 
 PHE   0.036   0.003   PHE A  84 
 TRP   0.013   0.002   TRP L 286 
 HIS   0.020   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00703 /  0.31 (18335)
  covalent geometry    : angle       0.91341 /  0.50 (26055)
  hydrogen bonds       : bond        0.08899 /  5.93 (  859)
  hydrogen bonds       : angle       5.34397 /  3.92 ( 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
  175 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 84
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8699 (tt0)
REVERT: A  131 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8425 (ttp80)
REVERT: B   35 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7716 (mmt90)
REVERT: C   95 LYS cc_start: 0.8547 (tppt) cc_final: 0.8154 (tptp)
REVERT: D   98 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8579 (mp)
REVERT: E   83 ARG cc_start: 0.1794 (OUTLIER) cc_final: 0.1446 (mtp-110)
REVERT: G   78 ILE cc_start: 0.1823 (OUTLIER) cc_final: 0.1575 (mt)
REVERT: H   34 TYR cc_start: 0.1306 (OUTLIER) cc_final: 0.0546 (m-10)
REVERT: H   79 HIS cc_start: 0.1189 (OUTLIER) cc_final: 0.0271 (t70)
REVERT: N   65 HIS cc_start: 0.3801 (OUTLIER) cc_final: 0.3448 (m90)
REVERT: N  167 TYR cc_start: 0.2603 (OUTLIER) cc_final: 0.1494 (m-10)
REVERT: N  259 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5454 (t80)
REVERT: N  286 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7191 (tt)
  outliers start: 91
  outliers final: 54
  residues processed: 162
  average time/residue: 0.1488
  time to fit residues: 35.5815
Evaluate side-chains
  138 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 72
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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   35 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   73 THR
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   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 E residue  107 THR
Chi-restraints excluded: chain F residue   26 ILE
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   76 THR
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   41 VAL
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   79 HIS
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 L residue  155 ILE
Chi-restraints excluded: chain L residue  293 ILE
Chi-restraints excluded: chain L residue  301 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  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  286 LEU
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 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:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 158 optimal weight:    0.4980
   chunk 115 optimal weight:    9.9990
   chunk 118 optimal weight:    2.9990
   chunk 130 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 157 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 110 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 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 = 0.4842 r_free = 0.4842 target = 0.241067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.211100 restraints weight = 75186.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.208981 restraints weight = 72413.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.206016 restraints weight = 52090.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.205560 restraints weight = 53974.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.204815 restraints weight = 46573.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4462 r_free = 0.4462    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4462 r_free = 0.4462    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6257
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  18335  Z= 0.157
  Angle     :  0.684  11.977  26055  Z= 0.384
  Chirality :  0.048   0.309   2972
  Planarity :  0.005   0.057   2279
  Dihedral  : 29.802 176.345   4793
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 23.73 %
    Favored  : 72.24 %
  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: -1.82 (0.22), residues: 1418
  helix:  0.01 (0.22), residues: 527
  sheet: -0.93 (0.37), residues: 215
  loop : -2.34 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  83 
 TYR   0.014   0.001   TYR L 131 
 PHE   0.018   0.001   PHE N 213 
 TRP   0.016   0.001   TRP L 286 
 HIS   0.010   0.001   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.16 (18335)
  covalent geometry    : angle       0.68357 /  0.38 (26055)
  hydrogen bonds       : bond        0.06457 /  4.33 (  859)
  hydrogen bonds       : angle       4.58059 /  3.35 ( 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
  132 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 83
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8361 (tt0)
REVERT: A  131 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8211 (ttp80)
REVERT: C   95 LYS cc_start: 0.8485 (tppt) cc_final: 0.8156 (tptp)
REVERT: D   98 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8424 (mp)
REVERT: N  166 ILE cc_start: -0.0901 (OUTLIER) cc_final: -0.1803 (mm)
REVERT: N  167 TYR cc_start: 0.2543 (OUTLIER) cc_final: 0.1503 (m-10)
REVERT: N  259 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5455 (t80)
  outliers start: 49
  outliers final: 28
  residues processed: 123
  average time/residue: 0.1521
  time to fit residues: 27.5148
Evaluate side-chains
  110 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 76
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
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   66 ILE
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  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   84 PHE
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   64 GLU
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 L residue   88 LEU
Chi-restraints excluded: chain L residue  301 THR
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   66 ILE
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  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 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:    8.9990
   chunk 149 optimal weight:    0.8980
   chunk 141 optimal weight:    7.9990
   chunk 156 optimal weight:    6.9990
   chunk 86 optimal weight:   30.0000
   chunk 0 optimal weight:    7.9990
   chunk 96 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 148 optimal weight:    7.9990
   overall best weight:    3.9788

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.233583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.200636 restraints weight = 62860.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.198784 restraints weight = 79249.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.197451 restraints weight = 64449.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.197101 restraints weight = 62399.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.196687 restraints weight = 49745.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4343 r_free = 0.4343    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4343 r_free = 0.4343    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4343
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.6046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.103  18335  Z= 0.373
  Angle     :  0.965  11.572  26055  Z= 0.519
  Chirality :  0.063   0.395   2972
  Planarity :  0.008   0.069   2279
  Dihedral  : 30.072 178.316   4791
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.13 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 20.82 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -0.69 (0.21), residues: 519
  sheet: -1.04 (0.39), residues: 201
  loop : -2.49 (0.22), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  69 
 TYR   0.033   0.004   TYR F  88 
 PHE   0.037   0.003   PHE A  84 
 TRP   0.009   0.002   TRP L  95 
 HIS   0.024   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00851 /  0.37 (18335)
  covalent geometry    : angle       0.96485 /  0.52 (26055)
  hydrogen bonds       : bond        0.10626 /  7.04 (  859)
  hydrogen bonds       : angle       5.49661 /  4.03 ( 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
  159 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 76
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8858 (tt0)
REVERT: A  131 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8375 (ttp80)
REVERT: C   74 LYS cc_start: 0.8245 (mppt) cc_final: 0.7605 (mmtp)
REVERT: D   98 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8658 (mp)
REVERT: E   83 ARG cc_start: 0.1019 (mtp180) cc_final: 0.0600 (mtp85)
REVERT: N   15 GLU cc_start: 0.0650 (OUTLIER) cc_final: 0.0402 (mt-10)
REVERT: N  167 TYR cc_start: 0.2838 (OUTLIER) cc_final: 0.1515 (m-10)
REVERT: N  201 ILE cc_start: 0.3438 (OUTLIER) cc_final: 0.3205 (mp)
REVERT: N  259 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5665 (t80)
  outliers start: 83
  outliers final: 47
  residues processed: 151
  average time/residue: 0.1394
  time to fit residues: 31.5953
Evaluate side-chains
  128 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 74
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
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 A residue  131 ARG
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 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   38 ASN
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  102 ILE
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   61 LEU
Chi-restraints excluded: chain F residue   62 LEU
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  100 VAL
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  106 HIS
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain L residue   88 LEU
Chi-restraints excluded: chain L residue  301 THR
Chi-restraints excluded: chain N residue   15 GLU
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  144 VAL
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  201 ILE
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
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:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 98 optimal weight:   30.0000
   chunk 66 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 71 optimal weight:   30.0000
   chunk 28 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 147 optimal weight:    9.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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  46 HIS
** 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 = 0.4807 r_free = 0.4807 target = 0.236796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.206281 restraints weight = 73953.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.204175 restraints weight = 76334.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.202873 restraints weight = 57207.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.202693 restraints weight = 55042.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.202106 restraints weight = 45722.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4439 r_free = 0.4439    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4439 r_free = 0.4439    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.4439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          0.6007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  18335  Z= 0.166
  Angle     :  0.694  10.106  26055  Z= 0.391
  Chirality :  0.049   0.307   2972
  Planarity :  0.005   0.057   2279
  Dihedral  : 29.826 176.222   4791
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 23.65 %
    Favored  : 72.24 %
  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: -1.84 (0.22), residues: 1418
  helix: -0.04 (0.22), residues: 524
  sheet: -1.03 (0.37), residues: 215
  loop : -2.28 (0.22), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  83 
 TYR   0.018   0.002   TYR C  39 
 PHE   0.023   0.001   PHE E  67 
 TRP   0.017   0.001   TRP L 286 
 HIS   0.050   0.002   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.17 (18335)
  covalent geometry    : angle       0.69422 /  0.39 (26055)
  hydrogen bonds       : bond        0.06962 /  4.69 (  859)
  hydrogen bonds       : angle       4.72157 /  3.45 ( 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
  138 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 88
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8576 (tt0)
REVERT: A  131 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8188 (ttp80)
REVERT: C   74 LYS cc_start: 0.8079 (mppt) cc_final: 0.7631 (mmtp)
REVERT: D   98 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8484 (mp)
REVERT: N  201 ILE cc_start: 0.3333 (OUTLIER) cc_final: 0.3102 (mp)
REVERT: N  259 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.5308 (t80)
  outliers start: 50
  outliers final: 33
  residues processed: 130
  average time/residue: 0.1396
  time to fit residues: 27.7538
Evaluate side-chains
  121 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 ILE
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   83 LEU
Chi-restraints excluded: chain C residue  101 THR
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   84 PHE
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  116 THR
Chi-restraints excluded: chain L residue   88 LEU
Chi-restraints excluded: chain L residue  301 THR
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue  134 MET
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  192 THR
Chi-restraints excluded: chain N residue  201 ILE
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  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
Chi-restraints excluded: chain O residue   55 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 143 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 151 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 23 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   chunk 132 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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
D  81 ASN
F  25 ASN
H  81 ASN
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4830 r_free = 0.4830 target = 0.238916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.206886 restraints weight = 77155.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.204997 restraints weight = 78468.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.203802 restraints weight = 52549.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.203400 restraints weight = 50965.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.202879 restraints weight = 44454.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4451
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4451 r_free = 0.4451    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4450 r_free = 0.4450    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (10 function evaluations)
r_final: 0.4450
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6302
moved from start:          0.6073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  18335  Z= 0.143
  Angle     :  0.651  14.313  26055  Z= 0.366
  Chirality :  0.046   0.241   2972
  Planarity :  0.004   0.052   2279
  Dihedral  : 29.606 176.897   4789
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 24.37 %
    Favored  : 72.15 %
  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: -1.41 (0.22), residues: 1418
  helix:  0.49 (0.22), residues: 528
  sheet: -0.83 (0.38), residues: 215
  loop : -2.19 (0.23), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  53 
 TYR   0.013   0.001   TYR H  80 
 PHE   0.019   0.001   PHE N 213 
 TRP   0.016   0.001   TRP L 286 
 HIS   0.019   0.001   HIS H 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.14 (18335)
  covalent geometry    : angle       0.65074 /  0.37 (26055)
  hydrogen bonds       : bond        0.06045 /  4.03 (  859)
  hydrogen bonds       : angle       4.27156 /  3.11 ( 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
  129 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 87
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8392 (tt0)
REVERT: A  131 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8040 (ttp80)
REVERT: C   16 THR cc_start: 0.6570 (OUTLIER) cc_final: 0.6351 (t)
REVERT: L  107 ASP cc_start: 0.3445 (m-30) cc_final: 0.2167 (t0)
REVERT: N  259 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5361 (t80)
  outliers start: 42
  outliers final: 30
  residues processed: 120
  average time/residue: 0.1423
  time to fit residues: 25.6631
Evaluate side-chains
  116 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  117 VAL
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   83 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   84 PHE
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   93 THR
Chi-restraints excluded: chain H residue  105 LYS
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue  301 THR
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue  134 MET
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  199 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  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:    0.9990
   chunk 144 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 87 optimal weight:   20.0000
   chunk 3 optimal weight:    0.6980
   chunk 116 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 114 optimal weight:   10.0000
   chunk 132 optimal weight:    0.8980
   chunk 72 optimal weight:   30.0000
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.238095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.205829 restraints weight = 77491.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.202495 restraints weight = 72894.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.200964 restraints weight = 57895.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.201375 restraints weight = 49669.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.201023 restraints weight = 40877.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.4416
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4416 r_free = 0.4416    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4416 r_free = 0.4416    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4416
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6356
moved from start:          0.6201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18335  Z= 0.143
  Angle     :  0.642  10.264  26055  Z= 0.361
  Chirality :  0.046   0.241   2972
  Planarity :  0.004   0.052   2279
  Dihedral  : 29.546 176.669   4787
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 25.34 %
    Favored  : 71.75 %
  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: -1.27 (0.22), residues: 1418
  helix:  0.62 (0.22), residues: 532
  sheet: -0.78 (0.38), residues: 215
  loop : -2.13 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  42 
 TYR   0.012   0.001   TYR F  88 
 PHE   0.019   0.001   PHE E  67 
 TRP   0.013   0.001   TRP L 286 
 HIS   0.016   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.14 (18335)
  covalent geometry    : angle       0.64192 /  0.36 (26055)
  hydrogen bonds       : bond        0.05984 /  4.00 (  859)
  hydrogen bonds       : angle       4.21798 /  3.08 ( 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
  114 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 79
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8425 (tt0)
REVERT: A  131 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8157 (ttp80)
REVERT: C   16 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.6457 (t)
REVERT: C   74 LYS cc_start: 0.8399 (mmtp) cc_final: 0.8131 (mmtm)
REVERT: E   97 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7821 (mp0)
REVERT: L  107 ASP cc_start: 0.3739 (m-30) cc_final: 0.2269 (t0)
REVERT: N  259 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.5394 (t80)
  outliers start: 35
  outliers final: 28
  residues processed: 110
  average time/residue: 0.1453
  time to fit residues: 24.0271
Evaluate side-chains
  111 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  102 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   97 GLU
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   93 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue  301 THR
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue  134 MET
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  199 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  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
Chi-restraints excluded: chain O residue   55 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 52 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 148 optimal weight:    0.0470
   chunk 62 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    1.1282

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.238320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.204438 restraints weight = 66190.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.202859 restraints weight = 77761.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.201176 restraints weight = 55353.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.200973 restraints weight = 55792.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.200611 restraints weight = 42191.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4393 r_free = 0.4393    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4393 r_free = 0.4393    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.6365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  18335  Z= 0.155
  Angle     :  0.651  11.360  26055  Z= 0.363
  Chirality :  0.046   0.243   2972
  Planarity :  0.004   0.051   2279
  Dihedral  : 29.528 176.996   4787
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 25.26 %
    Favored  : 71.83 %
  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: -1.26 (0.22), residues: 1418
  helix:  0.63 (0.22), residues: 532
  sheet: -0.76 (0.38), residues: 215
  loop : -2.14 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 129 
 TYR   0.013   0.001   TYR F  88 
 PHE   0.017   0.001   PHE E  67 
 TRP   0.014   0.001   TRP L 286 
 HIS   0.014   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 (18335)
  covalent geometry    : angle       0.65116 /  0.36 (26055)
  hydrogen bonds       : bond        0.06148 /  4.11 (  859)
  hydrogen bonds       : angle       4.20945 /  3.07 ( 2148)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2633.88 seconds
wall clock time: 46 minutes 26.94 seconds (2786.94 seconds total)